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Fristot E, Cambray G, Bonnet J. LactoSpanks: A Collection of IPTG Inducible Promoters for the Commensal Lactic Acid Bacteria Lactobacillus gasseri. ACS Synth Biol 2024; 13:951-957. [PMID: 38335132 DOI: 10.1021/acssynbio.3c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Lactic acid bacteria (LAB) are important for many biotechnological applications such as bioproduction and engineered probiotics for therapy. Inducible promoters are key gene expression control elements, yet those available in LAB are mainly based on bacteriocin systems and have many drawbacks, including large gene clusters, costly inducer peptides, and little portability to in vivo settings. Using Lactobacillus gasseri, a model commensal bacteria from the human gut, we report the engineering of synthetic LactoSpanks promoters (Pls), a collection of variable strength inducible promoters controlled by the LacI repressor from E. coli and induced by isopropyl β-d-1-thiogalactopyranoside (IPTG). We first show that the Phyper-spank promoter from Bacillus subtilis is functional in L. gasseri, albeit with substantial leakage. We then construct and screen a semirational library of Phyper-spank variants to select a set of four IPTG-inducible promoters that span a range of expression levels and exhibit reduced leakages and operational dynamic ranges (from ca. 9 to 28 fold-change). With their low genetic footprint and simplicity of use, LactoSpanks will support many applications in L. gasseri, and potentially other lactic acid and Gram-positive bacteria.
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Affiliation(s)
- Elsa Fristot
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
| | - Guillaume Cambray
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), University of Montpellier, INRAE UMR1333, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre de Biologie Structurale (CBS), University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France
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Chen G, Lian W, Geng A, Wang Y, Liu M, Zhang Y, Wang X. pOsHAK1:OsSUT1 Promotes Sugar Transport and Enhances Drought Tolerance in Rice. Int J Mol Sci 2024; 25:2158. [PMID: 38396836 PMCID: PMC10889344 DOI: 10.3390/ijms25042158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Plant cells accumulate osmotic substances (e.g., sugar) to protect cell components and maintain osmotic balance under drought stress conditions. Previous studies found that pOsHAK1:OsFLN2 promotes sugar metabolism and improves the drought tolerance of rice plants under drought stress. This study further evaluated the effect of the ectopic expression of the OsSUT1 gene driven by the OsHAK1 promoter on the sugar transport and drought tolerance of rice. The results showed that the net photosynthetic rate and sucrose phosphate synthase activity of plants expressing the OsSUT1 gene were not significantly different from those of wild-type (WT) rice plants under drought conditions. However, the sucrose transport rate in the phloem increased in the transgenic plants, and the sucrose contents were significantly lower in the leaves but significantly higher in the roots of transgenic plants than those in WT plants. The pOsHAK1:OsSUT1 and pOsHAK1:OsFLN2 transgenic lines had similar rates of long-distance sucrose transport and drought tolerance, which were higher than those of the WT plants. The relative water content of the transgenic plants was higher, while their water loss rate, hydrogen peroxide (H2O2), and malondialdehyde (MDA) contents were lower than those of the WT plants. The stress-responsive gene OsbZIP23 and the antioxidant-related gene OsCATB were significantly upregulated in the drought-treated transgenic lines, while the senescence indicator gene SGR and the stress-responsive gene OsNAC2 were down-regulated compared to WT plants. These results showed that promoting the long-distance sugar transport through the expression of pOsHAK1:OsSUT1 could produce an improved drought tolerance effect similar to that of pOsHAK1:OsFLN2, providing an effective way to improve the drought tolerance of cereal crops at the seedling stage.
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Affiliation(s)
- Guang Chen
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Wenli Lian
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Anjing Geng
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yihan Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Minghao Liu
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yue Zhang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
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O'Laughlin R, Tran Q, Lezia A, Ngamkanjanarat W, Emmanuele P, Hao N, Hasty J. A Standardized Set of MoClo-Compatible Inducible Promoter Systems for Tunable Gene Expression in Yeast. ACS Synth Biol 2024; 13:85-102. [PMID: 38079574 DOI: 10.1021/acssynbio.3c00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Small-molecule control of gene expression underlies the function of numerous engineered gene circuits that are capable of environmental sensing, computation, and memory. While many recently developed inducible promoters have been tailor-made for bacteria or mammalian cells, relatively few new systems have been built for Saccharomyces cerevisiae, limiting the scale of synthetic biology work that can be done in yeast. To address this, we created the yeast Tunable Expression Systems Toolkit (yTEST), which contains a set of five extensively characterized inducible promoter systems regulated by the small-molecules doxycycline (Dox), abscisic acid (ABA), danoprevir (DNV), 1-naphthaleneacetic acid (NAA), and 5-phenyl-indole-3-acetic acid (5-Ph-IAA). Assembly was made to be compatible with the modular cloning yeast toolkit (MoClo-YTK) to enhance the ease of use and provide a framework to benchmark and standardize each system. Using this approach, we built multiple systems with maximal expression levels greater than those of the strong constitutive TDH3 promoter. Furthermore, each of the five classes of systems could be induced at least 60-fold after a 6 h induction and the highest fold change observed was approximately 300. Thus, yTEST provides a reliable, diverse, and customizable set of inducible promoters to modulate gene expression in yeast for applications in synthetic biology, metabolic engineering, and basic research.
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Affiliation(s)
- Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Quoc Tran
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Andrew Lezia
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Wasu Ngamkanjanarat
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Philip Emmanuele
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Nan Hao
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, United States
- Synthetic Biology Institute, University of California San Diego, La Jolla, California 92093, United States
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, United States
- Synthetic Biology Institute, University of California San Diego, La Jolla, California 92093, United States
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Sheshukova EV, Kamarova KA, Ershova NM, Komarova TV. Nicotiana benthamiana Methanol-Inducible Gene (MIG) 21 Encodes a Nucleolus-Localized Protein That Stimulates Viral Intercellular Transport and Downregulates Nuclear Import. Plants (Basel) 2024; 13:279. [PMID: 38256832 PMCID: PMC10819229 DOI: 10.3390/plants13020279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
The mechanical damage of plant tissues leads to the activation of methanol production and its release into the atmosphere. The gaseous methanol or vapors emitted by the damaged plant induce resistance in neighboring intact plants to bacterial pathogens but create favorable conditions for viral infection spread. Among the Nicotiana benthamiana methanol-inducible genes (MIGs), most are associated with plant defense and intercellular transport. Here, we characterize NbMIG21, which encodes a 209 aa protein (NbMIG21p) that does not share any homology with annotated proteins. NbMIG21p was demonstrated to contain a nucleolus localization signal (NoLS). Colocalization studies with fibrillarin and coilin, nucleolus and Cajal body marker proteins, revealed that NbMIG21p is distributed among these subnuclear structures. Our results show that recombinant NbMIG21 possesses DNA-binding properties. Similar to a gaseous methanol effect, an increased NbMIG21 expression leads to downregulation of the nuclear import of proteins with nuclear localization signals (NLSs), as was demonstrated with the GFP-NLS model protein. Moreover, upregulated NbMIG21 expression facilitates tobacco mosaic virus (TMV) intercellular transport and reproduction. We identified an NbMIG21 promoter (PrMIG21) and showed that it is methanol sensitive; thus, the induction of NbMIG21 mRNA accumulation occurs at the level of transcription. Our findings suggest that methanol-activated NbMIG21 might participate in creating favorable conditions for viral reproduction and spread.
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Affiliation(s)
- Ekaterina V. Sheshukova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (E.V.S.); (K.A.K.); (N.M.E.)
| | - Kamila A. Kamarova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (E.V.S.); (K.A.K.); (N.M.E.)
| | - Natalia M. Ershova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (E.V.S.); (K.A.K.); (N.M.E.)
| | - Tatiana V. Komarova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (E.V.S.); (K.A.K.); (N.M.E.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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Vidal L, Dong Z, Olofsson K, Karlsson EN, Nicaud JM. Production of Rhizopus oryzae lipase using optimized Yarrowia lipolytica expression system. FEMS Yeast Res 2023:foad037. [PMID: 37496194 PMCID: PMC10384013 DOI: 10.1093/femsyr/foad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023] Open
Abstract
Yarrowia lipolytica is an alternative yeast for heterologous protein production. Based on auto-cloning vectors, a set of 18 chromogenic cloning vectors was developed, each containing one of the excisable auxotrophic selective markers URA3ex, LYS5ex and LEU2ex, and one of six different promoters: the constitutive pTEF, the phase dependent hybrid pHp4d, and the erythritol-inducible promoters from pEYK1 and pEYL1 derivatives. These vectors allowed to increase the speed of cloning of the gene of interest. In parallel, an improved new rProt recipient strain JMY8647 was developed by abolishing filamentation and introducing an auxotrophy for lysine (Lys-), providing an additional marker for genetic engineering. Using this cloning strategy, the optimal targeting sequence for Rhizopus oryzae ROL lipase secretion was determined. Among the eight targeting sequences, the SP6 signal sequence resulted in a 23% improvement in the lipase activity compared to that obtained with the wild-type ROL signal sequence. Higher specific lipase activities were obtained using hybrid erythritol-inducible promoters pHU8EYK and pEYL1-5AB, 1.9 and 2.2 times respectively, when compared with the constitutive pTEF promoter. Two copy strains produce a 3.3 fold increase in lipase activity over the pTEF monocopy strain (266.7 mU/mg versus 79.7 mU/mg).
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Affiliation(s)
- Lea Vidal
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Zehui Dong
- Biotechnology, Department of Chemistry, Lund University, 221 00 Lund, Sweden
- AAK AB, Skrivaregatan 9, 215 32 Malmö, Sweden
| | | | | | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
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Markakiou S, Neves AR, Zeidan AA, Gaspar P. Development of a Tetracycline-Inducible System for Conditional Gene Expression in Lactococcus lactis and Streptococcus thermophilus. Microbiol Spectr 2023; 11:e0066823. [PMID: 37191512 PMCID: PMC10269922 DOI: 10.1128/spectrum.00668-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
Inducible gene expression systems are invaluable tools for the functional characterization of genes and in the construction of protein overexpression hosts. Controllable expression is especially important for the study of essential and toxic genes or genes where the level of expression tightly influences their cellular effect. Here, we implemented the well-characterized tetracycline-inducible expression system in two industrially important lactic acid bacteria, Lactococcus lactis and Streptococcus thermophilus. Using a fluorescent reporter gene, we show that optimization of the repression level is necessary for efficient induction using anhydrotetracycline in both organisms. Random mutagenesis in the ribosome binding site of the tetracycline repressor TetR in Lactococcus lactis indicated that altering the expression levels of TetR was necessary for efficient inducible expression of the reporter gene. Through this approach, we achieved plasmid-based, inducer-responsive, and tight gene expression in Lactococcus lactis. We then verified the functionality of the optimized inducible expression system in Streptococcus thermophilus following its chromosomal integration using a markerless mutagenesis approach and a novel DNA fragment assembly tool presented herein. This inducible expression system holds several advantages over other described systems in lactic acid bacteria, although more efficient techniques for genetic engineering are still needed to realize these advantages in industrially relevant species, such as S. thermophilus. Our work expands the molecular toolbox of these bacteria, which can accelerate future physiological studies. IMPORTANCE Lactococcus lactis and Streptococcus thermophilus are two industrially important lactic acid bacteria globally used in dairy fermentations and, therefore, are of considerable commercial interest to the food industry. Moreover, due to their general history of safe usage, these microorganisms are increasingly being explored as hosts for the production of heterologous proteins and various chemicals. Development of molecular tools in the form of inducible expression systems and mutagenesis techniques facilitates their in-depth physiological characterization as well as their exploitation in biotechnological applications.
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Affiliation(s)
- Sofia Markakiou
- R&D Department, Chr. Hansen A/S, Hørsholm, Denmark
- Department of Biochemistry, University of Groningen, Groningen, Netherlands
| | | | | | - Paula Gaspar
- R&D Department, Chr. Hansen A/S, Hørsholm, Denmark
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Klotz A, Kaczmarczyk A, Jenal U. A Synthetic Cumate- Inducible Promoter for Graded and Homogenous Gene Expression in Pseudomonas aeruginosa. Appl Environ Microbiol 2023:e0021123. [PMID: 37199671 DOI: 10.1128/aem.00211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Inducible gene expression systems are powerful genetic tools to study bacterial physiology, probing essential and toxic gene functions, gene dosage effects, and overexpression phenotypes. For the opportunistic human pathogen Pseudomonas aeruginosa, dedicated inducible gene expression systems are scarce. In the current study, we developed a minimal synthetic 4-isopropylbenzoic acid (cumate)-inducible promoter, called PQJ, that is tunable over several orders of magnitude. This was achieved by combining semirandomized housekeeping promoter libraries and control elements from the Pseudomonas putida strain F1 cym/cmt system with powerful fluorescence-activated cell sorting (FACS) to select functionally optimized variants. Using flow cytometry and live-cell fluorescence microscopy, we demonstrate that PQJ responds rapidly and homogenously to the inducer cumate in a graded manner at the single-cell level. PQJ and cumate are orthogonal to the frequently used isopropyl β-d-thiogalactopyranoside (IPTG)-regulated lacIq-Ptac expression system. The modular design of the cumate-inducible expression cassette together with the FACS-based enrichment strategy presented here facilitates portability, thus serving as a blueprint for the development of tailored gene expression systems for a wide range of bacteria. IMPORTANCE Reverse genetics is a powerful approach to study bacterial physiology and behavior by relying on well-developed genetic tools, such as inducible promoters. For the human pathogen Pseudomonas aeruginosa, well-characterized inducible promoters are scarce. In the current work, we used a synthetic biology-based approach to develop a cumate-inducible promoter for P. aeruginosa, termed PQJ, that shows excellent induction properties at the single-cell level. This genetic tool provides the means for qualitative and quantitative gene function studies describing P. aeruginosa's physiology and virulence in vitro and in vivo. Because this synthetic approach to constructing species-specific inducible promoters is portable, it can serve as a blueprint for similar tailored gene expression systems in bacteria largely lacking such tools, including, for example, representatives of the human microbiota.
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Affiliation(s)
| | | | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
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Chang X, Yang M, Li H, Wu J, Zhang J, Yin C, Ma W, Chen H, Zhou F, Lin Y. Cloning of the promoter of rice brown planthopper feeding-inducible gene OsTPS31 and identification of related cis-regulatory elements. Pest Manag Sci 2023; 79:1809-1819. [PMID: 36637212 DOI: 10.1002/ps.7356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Brown planthopper (BPH; Nilaparvata lugens) is one of the most serious pests of rice in the world. Insect-resistant genetic engineering is a very effective technology to control BPH. The promoters and cis-regulatory elements inducible by plant-feeding insects are critical for genetic engineering of insect-resistant crops. RESULTS In this study, we cloned a promoter Ptps31 and a 7 bp cis-regulatory sequence that up-regulated downstream genes induced by BPH feeding. The promoter of OsTPS31 (Ptps31) unresponsive to physical damage but responsive to BPH feeding was cloned and functionally verified. The results showed that expression of the OsBPH14 gene driven by the promoter region from -510 to -246 bp in rice could significantly improve the resistance to BPH. The promoter region from -376 to -370 bp (TAGTGTC) was identified as a cis-regulatory sequence related to BPH feeding induction of downstream gene expression. CONCLUSION The findings provide a new promoter and a new cis-regulatory sequence tool for the research on and application of rice BPH resistance genes, as well as a new perspective for functional analysis of the OsTPS31 gene. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xinlei Chang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mei Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hanpeng Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiemin Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Changxi Yin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Kim MJ, Kim SH, Abdellaoui N, Choi TJ. Isolation and Characterization of a Salt Inducible Promoter from Chlorella vulgaris PKVL7422. J Microbiol Biotechnol 2023; 33:1-9. [PMID: 37164686 PMCID: PMC10394332 DOI: 10.4014/jmb.2304.04005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
Chlorella is a eukaryotic organism that can be used as an industrial host to produce recombinant proteins. In this study, a salt-inducible promoter (SIP) was isolated from the freshwater species Chlorella vulgaris PKVL7422 from the screening of genes that were upregulated after salt treatment. Several cis-acting elements, including stress response elements, were identified in the isolated SIP. Moreover, the Gaussia luciferase gene was cloned after the SIP and transformed into C. vulgaris to test the inducibility of this promoter. Reexamination of transcriptome of C. vulgaris revealed that genes involved in the synthesis of methyl jasmonic acid (MeJA), gibberellin (GA), and abscisic acid (ABA) were up-regulated when C. vulgaris was-treated with salt. Furthermore, the expression level of recombinant luciferase increased when the transformed C. vulgaris was treated with salt and MeJA, GA, and ABA. This study represents the first report of the C. vulgaris SIP and highlights how transformed microalgae could be used for robust expression of recombinant proteins.
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Affiliation(s)
- Min-Jeong Kim
- School of Marine and Fisheries Sciences, Pukyong National University, Busan, Republic of Korea
| | - Su-Hyun Kim
- School of Marine and Fisheries Sciences, Pukyong National University, Busan, Republic of Korea
| | - Najib Abdellaoui
- School of Marine and Fisheries Sciences, Pukyong National University, Busan, Republic of Korea
- Department of Biological Sciences, Kongju National University, Kongju 32588, Republic of Korea
| | - Tae-Jin Choi
- School of Marine and Fisheries Sciences, Pukyong National University, Busan, Republic of Korea
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Tabilo-Agurto C, Del Rio-Pinilla V, Eltit-Villarroel V, Goity A, Muñoz-Guzmán F, Larrondo LF. Developing a Temperature-Inducible Transcriptional Rheostat in Neurospora crassa. mBio 2023; 14:e0329122. [PMID: 36744948 DOI: 10.1128/mbio.03291-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Heat shock protein (HSP)-encoding genes (hsp), part of the highly conserved heat shock response (HSR), are known to be induced by thermal stress in several organisms. In Neurospora crassa, three hsp genes, hsp30, hsp70, and hsp80, have been characterized; however, the role of defined cis elements in their responses to discrete changes in temperature remains largely unexplored. To fill this gap, while also aiming to obtain a reliable fungal heat shock-inducible system, we analyzed different sections of each hsp promoter by assessing the expression of real-time transcriptional reporters. Whereas all three promoters and their resected versions were acutely induced by high temperatures, only hsp30 displayed a broad range of expression and high tunability, amply exceeding other inducible promoter systems existing in Neurospora, such as quinic acid- or light-inducible ones. As proof of concept, we employed one of these promoters to control the expression of clr-2, which encodes the master regulator of Neurospora cellulolytic capabilities. The resulting strain fails to grow on cellulose at 25°C, whereas it grows robustly if heat shock pulses are delivered daily. Additionally, we designed two hsp30 synthetic promoters and characterized them, as well as the native promoters, using a gradient of high temperatures, yielding a wide range of responses to thermal stimuli. Thus, Neurospora hsp30-based promoters represent a new set of modular elements that can be used as transcriptional rheostats to adjust the expression of a gene of interest or for the implementation of regulated circuitries for synthetic biology and biotechnological strategies. IMPORTANCE A timely and dynamic response to strong temperature fluctuations is paramount for organismal biology. At the same time, inducible promoters are a powerful tool for fungal biotechnological and synthetic biology endeavors. In this work, we analyzed the activity of several N. crassa heat shock protein (hsp) promoters at a wide range of temperatures, observing that hsp30 exhibits remarkable sensitivity and a dynamic range of expression as we charted the response of this promoter to subtle increases in temperature, and also as we built and analyzed synthetic promoters based on hsp30 cis elements. As proof of concept, we tested the ability of hsp30 to provide tight control of a central process, cellulose degradation. While this study provides an unprecedented description of the regulation of the N. crassa hsp genes, it also contributes a noteworthy addition to the molecular toolset of transcriptional controllers in filamentous fungi.
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Zhuang Y, Sharif Y, Zeng X, Chen S, Chen H, Zhuang C, Deng Y, Ruan M, Chen S, Weijian Z. Molecular cloning and functional characterization of the promoter of a novel Aspergillus flavus inducible gene ( AhOMT1) from peanut. Front Plant Sci 2023; 14:1102181. [PMID: 36844094 PMCID: PMC9947529 DOI: 10.3389/fpls.2023.1102181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Peanut is an important oil and food legume crop grown in more than one hundred countries, but the yield and quality are often impaired by different pathogens and diseases, especially aflatoxins jeopardizing human health and causing global concerns. For better management of aflatoxin contamination, we report the cloning and characterization of a novel A. flavus inducible promoter of the O-methyltransferase gene (AhOMT1) from peanut. The AhOMT1 gene was identified as the highest inducible gene by A. flavus infection through genome-wide microarray analysis and verified by qRT-PCR analysis. AhOMT1 gene was studied in detail, and its promoter, fussed with the GUS gene, was introduced into Arabidopsis to generate homozygous transgenic lines. Expression of GUS gene was studied in transgenic plants under the infection of A. flavus. The analysis of AhOMT1 gene characterized by in silico assay, RNAseq, and qRT-PCR revealed minute expression in different organs and tissues with trace or no response to low temperature, drought, hormones, Ca2+, and bacterial stresses, but highly induced by A. flavus infection. It contains four exons encoding 297 aa predicted to transfer the methyl group of S-adenosyl-L-methionine (SAM). The promoter contains different cis-elements responsible for its expression characteristics. Functional characterization of AhOMT1P in transgenic Arabidopsis plants demonstrated highly inducible behavior only under A. flavus infection. The transgenic plants did not show GUS expression in any tissue(s) without inoculation of A. flavus spores. However, GUS activity increased significantly after inoculation of A. flavus and maintained a high level of expression after 48 hours of infection. These results provided a novel way for future management of peanut aflatoxins contamination through driving resistance genes in A. flavus inducible manner.
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Affiliation(s)
- Yuhui Zhuang
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yasir Sharif
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohong Zeng
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Suzheng Chen
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hua Chen
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chunhong Zhuang
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Deng
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | | | - Zhuang Weijian
- Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Azizoğlu A, Loureiro C, Venetz J, Brent R. Autorepression-Based Conditional Gene Expression System in Yeast for Variation-Suppressed Control of Protein Dosage. Curr Protoc 2023; 3:e647. [PMID: 36708363 DOI: 10.1002/cpz1.647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Conditional control of gene expression allows an experimenter to investigate many aspects of a gene's function. In the model organism Saccharomyces cerevisiae, a number of methods to control gene expression are widely practiced, including induction by metabolites, small molecules, and even light. However, all current methods suffer from at least one of a set of drawbacks, including need for specialized growth conditions, leaky expression, or requirement of specialized equipment. Here we describe protocols using two transformations to construct strains that carry a new controller in which all these drawbacks are overcome. In these strains, the expression of a controlled gene of interest is repressed by the bacterial repressor TetR and induced by anhydrotetracycline. TetR also regulates its own expression, creating an autorepression loop. This autorepression allows tight control of gene expression and protein dosage with low cell-to-cell variation in expression. A second repressor, TetR-Tup1, prevents any leaky expression. We also present a protocol showing a particular workhorse application of such strains to generate synchronized cell populations. We turn off expression of the cell cycle regulator CDC20 completely, arresting the cell population, and then we turn it back on so that the synchronized cells resume cell cycle progression. This control system can be applied to any endogenous or exogenous gene for precise expression. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generating a parent WTC846 strain Basic Protocol 2: Generating a WTC846 strain with controlled expression of the targeted gene Alternate Protocol: CRISPR-mediated promoter replacement Basic Protocol 3: Cell cycle synchronization/arrest and release using the WTC846- K3 ::CDC20 strain.
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Affiliation(s)
- Aslı Azizoğlu
- Computational Systems Biology and Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Cristina Loureiro
- Computational Systems Biology and Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Jonathan Venetz
- Computational Systems Biology and Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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13
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Niu X, Lu H, Fan Y, Wang W, Yuan Y, Hawkins M, Zhang J, Ye Z, Miao M, Liu Y, Xiao F. Manipulation of the transcription factor SlNAC1 for improved tolerance to abiotic stress in tomato. Plant Cell Environ 2022; 45:3537-3550. [PMID: 36128662 DOI: 10.1111/pce.14437] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/15/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
The tomato transcription factor SlNAC1 plays an important role in abiotic stress response and is fine-tuned at both transcriptional and posttranslational levels. The SlNAC1 gene is strongly induced by multiple abiotic stresses and the SlNAC1 protein is subjected to ubiquitin proteasome-mediated degradation. We found here that SlNAC1 possesses two distinct transactivation domains (TADs), TAD1 and TAD2. Significantly, the instability of SlNAC1 was attributed to the acidic amino acid-rich TAD1, in which the instability and transcriptional potential of TAD1 functionally overlapped; whereas the glutamine-rich TAD2 was stable and accounted for the abiotic stress signalling mediated by SlNAC1. Towards the goal of enhanced tolerance to abiotic stress in tomatoes, we manipulated SlNAC1 at both gene and protein levels: we generated a stable and functional SlNAC1 mutant SlNAC1∆191-270 by removing TAD1 and further engineered it to be stress-controllable by fusing the corresponding cDNA with the abiotic stress-inducible promoter ProStNAC1 . Transgenic tomato plants expressing the ProStNAC1 ::SlNAC1∆191-270 transgene did not display any undesired traits and exhibited enhanced tolerance to cold, drought and salt stresses. Taken together, our manipulation of the stress-related transcription factor via conditional expression of its derived stable and functional mutant provides a successful example for developing crops dynamically adapted to abiotic stress.
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Affiliation(s)
- Xiangli Niu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Han Lu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Youhong Fan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Wenjie Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Yulin Yuan
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Madigan Hawkins
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Min Miao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
| | - Yongsheng Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, China
- State Key Laboratory of Tea Plant Biology and Utilization, School of Horticulture, Anhui Agricultural University, Hefei, China
- Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Fangming Xiao
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, USA
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14
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Lin L, Fan J, Li P, Liu D, Ren S, Lin K, Fang Y, Lin C, Wang Y, Wu J. The Sclerotinia sclerotiorum- inducible promoter pBnGH17D7 in Brassica napus: isolation, characterization, and application in host-induced gene silencing. J Exp Bot 2022; 73:6663-6677. [PMID: 35927220 PMCID: PMC9629790 DOI: 10.1093/jxb/erac328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is among the most devastating diseases in Brassica napus worldwide. Conventional breeding for SSR resistance in Brassica species is challenging due to the limited availability of resistant germplasm. Therefore, genetic engineering is an attractive approach for developing SSR-resistant Brassica crops. Compared with the constitutive promoter, an S. sclerotiorum-inducible promoter would avoid ectopic expression of defense genes that may cause plant growth deficits. In this study, we generated a S. sclerotiorum-inducible promoter. pBnGH17D7, from the promoter of B. napus glycosyl hydrolase 17 gene (pBnGH17). Specifically, 5'-deletion and promoter activity analyses in transgenic Arabidopsis thaliana plants defined a 189 bp region of pBnGH17 which was indispensable for S. sclerotiorum-induced response. Compared with pBnGH17, pBnGH17D7 showed a similar response upon S. sclerotiorum infection, but lower activity in plant tissues in the absence of S. sclerotiorum infection. Moreover, we revealed that the transcription factor BnTGA7 directly binds to the TGACG motif in pBnGH17D7 to activate BnGH17. Ultimately, pBnGH17D7 was exploited for engineering Sclerotinia-resistant B. napus via host-induced gene silencing. It induces high expression of siRNAs against the S. sclerotiorum pathogenic factor gene specifically during infection, leading to increased resistance.
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Affiliation(s)
- Li Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Jialin Fan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Panpan Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Dongxiao Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Sichao Ren
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Keyun Lin
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Yujie Fang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Chen Lin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
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15
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Zhang G, Teng M, Liu S, Zhou J, Li J, DU G. [Directed evolution of maltose induced promoters with expanded gradient intensity]. Sheng Wu Gong Cheng Xue Bao 2022; 38:2606-2617. [PMID: 35871628 DOI: 10.13345/j.cjb.220251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Promoters with different sensitivity and response intensity are useful tools in gene expression regulation and metabolic engineering. Maltose induced promoter Pglvc was engineered to obtain promoters with different induced expression intensities. A promoter Pglvc mutant library was built by error-prone PCR, and screened by a growth-associated method using tetracycline resistance as an indicator. A library of promoter mutants with different sensitivity and intensity was obtained, and the maltose-induced response threshold range of promoter mutants (MT2, MT3, MT4, MT6) was extended from 0-3 g/L to 0-15 g/L. Among them, the highest induced expression intensity (MT8) was about 3.15 times higher than that of the original promoter for eGFP expression, which would be useful for its application in metabolic engineering and synthetic biology.
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Affiliation(s)
- Guoqiang Zhang
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Maofang Teng
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, Jiangsu, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Song Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, Jiangsu, China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, Jiangsu, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Guocheng DU
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, Jiangsu, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
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16
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Abstract
Chemically inducible gene expression systems have been an integral part of the advanced synthetic genetic circuit design and are employed for precise dynamic control over genetically engineered traits. However, the current systems for controlling transgene expression in most algae are limited to endogenous promoters that respond to different environmental factors. We developed a highly efficient, tunable, and reversible episome-based transcriptional control system in the model diatom alga, Phaeodactylum tricornutum. We assessed the time- and dose-response dynamics of each expression system using a reporter protein (eYFP) as a readout. Using our circuit configuration, we found two inducible expression systems with a high dynamic range and confirmed the suitability of an episome expression platform for synthetic biological applications in diatoms. These systems are controlled by the presence of β-estradiol and digoxin. Addition of either chemical to transgenic strains activates transcription with a dynamic range of up to ∼180-fold and ∼90-fold, respectively. We demonstrated that our episome-based transcriptional control systems are tunable and reversible in a dose- and time-dependent manner. Using droplet digital polymerase chain reaction (PCR), we also confirmed that inducer-dependent transcriptional activation starts within minutes of inducer application without any detectable transcript in the uninduced controls. The system described here expands the molecular and synthetic biology toolkits in algae and will facilitate future gene discovery and metabolic engineering efforts.
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Affiliation(s)
- Tessema K. Kassaw
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Andrew J. Paton
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Graham Peers
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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17
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Abstract
![]()
Filamentous fungi
are highly productive cell factories, often used
in industry for the production of enzymes and small bioactive compounds.
Recent years have seen an increasing number of synthetic-biology-based
applications in fungi, emphasizing the need for a synthetic biology
toolkit for these organisms. Here we present a collection of 96 genetic
parts, characterized in Penicillium or Aspergillus species, that are
compatible and interchangeable with the Modular Cloning system. The
toolkit contains natural and synthetic promoters (constitutive and
inducible), terminators, fluorescent reporters, and selection markers.
Furthermore, there are regulatory and DNA-binding domains of transcriptional
regulators and components for implementing different CRISPR-based
technologies. Genetic parts can be assembled into complex multipartite
assemblies and delivered through genomic integration or expressed
from an AMA1-sequence-based, fungal-replicating shuttle vector. With
this toolkit, synthetic transcription units with established promoters,
fusion proteins, or synthetic transcriptional regulation devices can
be more rapidly assembled in a standardized and modular manner for
novel fungal cell factories.
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Affiliation(s)
- László Mózsik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Carsten Pohl
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Yvonne Nygård
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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O'Neill CE, Skilton RJ, Forster J, Cleary DW, Pearson SA, Lampe DJ, Thomson NR, Clarke IN. An inducible transposon mutagenesis approach for the intracellular human pathogen Chlamydia trachomatis. Wellcome Open Res 2021; 6:312. [PMID: 35087955 PMCID: PMC8767425 DOI: 10.12688/wellcomeopenres.16068.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Chlamydia trachomatis is a prolific human pathogen that can cause serious long-term conditions if left untreated. Recent developments in Chlamydia genetics have opened the door to conducting targeted and random mutagenesis experiments to identify gene function. In the present study, an inducible transposon mutagenesis approach was developed for C. trachomatis using a self-replicating vector to deliver the transposon-transposase cassette - a significant step towards our ultimate aim of achieving saturation mutagenesis of the Chlamydia genome. Methods: The low transformation efficiency of C. trachomatis necessitated the design of a self-replicating vector carrying the transposon mutagenesis cassette (i.e. the Himar-1 transposon containing the beta lactamase gene as well as a hyperactive transposase gene under inducible control of the tet promoter system with the addition of a riboswitch). Chlamydia transformed with this vector (pSW2-RiboA-C9Q) were induced at 24 hours post-infection. Through dual control of transcription and translation, basal expression of transposase was tightly regulated to stabilise the plasmid prior to transposition. Results: Here we present the preliminary sequencing results of transposon mutant pools of both C. trachomatis biovars, using two plasmid-free representatives: urogenital strain C. trachomatis SWFP- and the lymphogranuloma venereum isolate L2(25667R). DNA sequencing libraries were generated and analysed using Oxford Nanopore Technologies' MinION technology. This enabled 'proof of concept' for the methods as an initial low-throughput screen of mutant libraries; the next step is to employ high throughput sequencing to assess saturation mutagenesis. Conclusions: This significant advance provides an efficient method for assaying C. trachomatis gene function and will enable the identification of the essential gene set of C. trachomatis. In the long-term, the methods described herein will add to the growing knowledge of chlamydial infection biology leading to the discovery of novel drug or vaccine targets.
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Affiliation(s)
- Colette E. O'Neill
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| | - Rachel J. Skilton
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| | - Jade Forster
- Cancer Sciences, University of Southampton, Southampton, SO16 6YD, UK
| | - David W. Cleary
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| | - Sarah A. Pearson
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
| | - David J. Lampe
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, 15116, USA
| | - Nicholas R. Thomson
- Bacterial Genomics and Evolution, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ian N. Clarke
- Clinical and Experimental Sciences, University of Southampton, Southampton, Hampshire, SO166YD, UK
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19
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Huang J, Chen J, Wang Y, Shi T, Ni X, Pu W, Liu J, Zhou Y, Cai N, Han S, Zheng P, Sun J. Development of a Hyperosmotic Stress Inducible Gene Expression System by Engineering the MtrA/MtrB-Dependent NCgl1418 Promoter in Corynebacterium glutamicum. Front Microbiol 2021; 12:718511. [PMID: 34367120 PMCID: PMC8334368 DOI: 10.3389/fmicb.2021.718511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Corynebacterium glutamicum is an important workhorse for industrial production of diversiform bioproducts. Precise regulation of gene expression is crucial for metabolic balance and enhancing production of target molecules. Auto-inducible promoters, which can be activated without expensive inducers, are ideal regulatory tools for industrial-scale application. However, few auto-inducible promoters have been identified and applied in C. glutamicum. Here, a hyperosmotic stress inducible gene expression system was developed and used for metabolic engineering of C. glutamicum. The promoter of NCgl1418 (P NCgl1418 ) that was activated by the two-component signal transduction system MtrA/MtrB was found to exhibit a high inducibility under hyperosmotic stress conditions. A synthetic promoter library was then constructed by randomizing the flanking and space regions of P NCgl1418 , and mutant promoters exhibiting high strength were isolated via fluorescence activated cell sorting (FACS)-based high-throughput screening. The hyperosmotic stress inducible gene expression system was applied to regulate the expression of lysE encoding a lysine exporter and repress four genes involved in lysine biosynthesis (gltA, pck, pgi, and hom) by CRISPR interference, which increased the lysine titer by 64.7% (from 17.0 to 28.0 g/L) in bioreactors. The hyperosmotic stress inducible gene expression system developed here is a simple and effective tool for gene auto-regulation in C. glutamicum and holds promise for metabolic engineering of C. glutamicum to produce valuable chemicals and fuels.
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Affiliation(s)
- Jingwen Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiuzhou Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tuo Shi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Wei Pu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yingyu Zhou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ningyun Cai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shuangyan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jibin Sun
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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20
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Hussnaetter KP, Philipp M, Müntjes K, Feldbrügge M, Schipper K. Controlling Unconventional Secretion for Production of Heterologous Proteins in Ustilago maydis through Transcriptional Regulation and Chemical Inhibition of the Kinase Don3. J Fungi (Basel) 2021; 7:jof7030179. [PMID: 33802393 PMCID: PMC7999842 DOI: 10.3390/jof7030179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/27/2022] Open
Abstract
Heterologous protein production is a highly demanded biotechnological process. Secretion of the product to the culture broth is advantageous because it drastically reduces downstream processing costs. We exploit unconventional secretion for heterologous protein expression in the fungal model microorganism Ustilago maydis. Proteins of interest are fused to carrier chitinase Cts1 for export via the fragmentation zone of dividing yeast cells in a lock-type mechanism. The kinase Don3 is essential for functional assembly of the fragmentation zone and hence, for release of Cts1-fusion proteins. Here, we are first to develop regulatory systems for unconventional protein secretion using Don3 as a gatekeeper to control when export occurs. This enables uncoupling the accumulation of biomass and protein synthesis of a product of choice from its export. Regulation was successfully established at two different levels using transcriptional and post-translational induction strategies. As a proof-of-principle, we applied autoinduction based on transcriptional don3 regulation for the production and secretion of functional anti-Gfp nanobodies. The presented developments comprise tailored solutions for differentially prized products and thus constitute another important step towards a competitive protein production platform.
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21
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Wang Y, Wang C, Rajaofera MJN, Zhu L, Xu X, Liu W, Zheng F, Miao W. WY195, a New Inducible Promoter From the Rubber Powdery Mildew Pathogen, Can Be Used as an Excellent Tool for Genetic Engineering. Front Microbiol 2020; 11:610252. [PMID: 33424812 PMCID: PMC7793764 DOI: 10.3389/fmicb.2020.610252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Until now, there are few studies and reports on the use of endogenous promoters of obligate biotrophic fungi. The WY195 promoter in the genome of Oidium heveae, the rubber powdery mildew pathogen, was predicted using PromoterScan and its promoter function was verified by the transient expression of the β-glucuronidase (GUS) gene. WY195 drove high levels of GUS expression in dicotyledons and monocotyledons. qRT-PCR indicated that GUS expression regulated by the WY195 promoter was 17.54-fold greater than that obtained using the CaMV 35S promoter in dicotyledons (Nicotiana tabacum), and 5.09-fold greater than that obtained using the ACT1 promoter in monocotyledons (Oryza sativa). Furthermore, WY195-regulated GUS gene expression was induced under high-temperature and drought conditions. Soluble proteins extracted from WY195-hpaXm transgenic tobacco was bioactive. Defensive micro-HR induced by the transgene expression of hpaXm was observed on transgenic tobacco leaves. Disease resistance bioassays showed that WY195-hpaXm transgenic tobacco enhanced the resistance to tobacco mosaic virus (TMV). WY195 has great potential for development as a new tool for genetic engineering. Further in-depth studies will help to better understand the transcriptional regulation mechanisms and the pathogenic mechanisms of O. heveae.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, China
| | - Chen Wang
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Mamy Jayne Nelly Rajaofera
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Li Zhu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Xinze Xu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Wenbo Liu
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Fucong Zheng
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
| | - Weiguo Miao
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
- College of Plant Protection, Hainan University, Haikou, China
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22
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Langa S, Peirotén Á, Arqués JL, Landete JM. Catabolite responsive elements as a strategy for the control of heterologous gene expression in lactobacilli. Appl Microbiol Biotechnol 2021; 105:225-33. [PMID: 33215257 DOI: 10.1007/s00253-020-11010-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/28/2020] [Accepted: 11/08/2020] [Indexed: 10/23/2022]
Abstract
Genes involved in the transport and catabolism of carbohydrates are usually controlled through the binding of the catabolite control protein A (CcpA) to the catabolite-responsive elements (cre) of target genes in Gram-positive bacteria. In this work, we show how the elimination of the cre sites in Lactobacillus casei BL23 promoters induced by sorbitol (PgutF), maltose (PmalL), and myo-inositol (PiolT) allowed the induction of gene expression in media supplemented with sorbitol, maltose, and myo-inositol, respectively, even in the presence of glucose. This was studied using plasmids encoding the anaerobic fluorescent protein evoglow-Pp1 as a reporter. In addition, gutF cre site was introduced into a bile inducible promoter (P16090) and into the constitutive promoter of the elongation factor P (PEf-P) of L. casei BL23. The existence of the cre site blocked gene expression in the P16090 inducible promoter in the presence of glucose, while it had no influence on the expression of the PEf-P constitutive one. These results demonstrated that the introduction or elimination of cre sites in inducible promoters allows the control and modification of their heterologous genetic expression, showing how the cre site, the transcriptional regulator, and CcpA interact to control gene expression in inducible genes. KEY POINTS: • Cre sequences regulate gene expression in inducible promoters in L. casei BL23. • Cre sites do not affect gene expression in constitutive promoters in L. casei BL23. • Cre sequences could control heterologous genic expression in lactobacilli.
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23
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Xiong X, Chen S. Expanding Toolbox for Genes Expression of Yarrowia lipolytica to Include Novel Inducible, Repressible, and Hybrid Promoters. ACS Synth Biol 2020; 9:2208-2213. [PMID: 32584553 DOI: 10.1021/acssynbio.0c00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Promoters are critical tools to precisely control gene expression for both synthetic biology and metabolic engineering. Although Yarrowia lipolytica has demonstrated many industrially relevant advantages, promoter discovery efforts on this non-conventional yeast are limited due to the challenge in finding suitable inducible and repressible promoters. Six copper-inducible promoters and five repressible promoters were isolated in this work. Especially, Cu2+-repressible promoters showed relatively high activity under non-repressing conditions compared with a constitutive promoter, but the strength could be almost fully repressed by a supplement of a low content of Cu2+. The six Cu2+-inducible promoters were engineered to improve their dynamic regulation range with a tandem upstream activation sequence. An engineered promoter was successfully used to construct a more productive pathway for production of a novel bioproduct, wax ester, than that used for both Cu2+-inducible promoter and constitutive promoter. This study provides effective tools applicable to fine-tune the gene expression in this microbial host.
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Affiliation(s)
- Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, Washington 99164, United States
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24
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Sun L, Wang J, Jiang W, Li Y, Zhang L, Ding Z, Gu Z, Shi G, Xu S. [Construction of a highly efficient synthetic lycopene engineered Saccharomyces cerevisiae]. Sheng Wu Gong Cheng Xue Bao 2020; 36:1334-1345. [PMID: 32748591 DOI: 10.13345/j.cjb.190524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lycopene, as a high value-added terpene compound, has been widely concerned by researchers at home and abroad. Firstly, the ability of lycopene synthesis of Saccharomyces cerevisiae model strains S288c and YPH499 was analyzed and compared. The results showed that YPH499 was more suitable for lycopene synthesis as yeast chassis. Subsequently, the effects of constitutive promoters GPDpr, TEF1pr and inducible promoters GAL1pr, GAL10pr on Lycopene synthesis were compared. The results showed that when GPDpr and TEF1pr were used as promoters of crtE, crtB and crtI in lycopene synthesis pathway, the production of lycopene was 15.31 mg/L after 60 h fermentation in shaking flask. When GAL1pr and GAL10pr were used as promoters, the production was 123.89 mg/L, which was 8.09 times higher. In addition, the methylvaleric acid (MVA) pathway was further modified to overexpress the key enzyme gene of N-terminal truncation, tHMG1 (3-hydroxy-3-methylglutaryl coenzyme A reductase). The lycopene production was 265.68 mg/L, and the yield per cell was 72.79 mg/g. The Saccharomyces cerevisiae strain designed and constructed in this study can express lycopene in high yield per cell, thus could be used in the industrial production of lycopene after further construction and optimization.
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Affiliation(s)
- Ling Sun
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Junhua Wang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wei Jiang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Youran Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Liang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhongyang Ding
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhenghua Gu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Guiyang Shi
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.,School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
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Callaghan JD, Stella NA, Lehner KM, Treat BR, Brothers KM, St Leger AJ, Shanks RMQ. Xylose- Inducible Promoter Tools for Pseudomonas Species and Their Use in Implicating a Role for the Type II Secretion System Protein XcpQ in the Inhibition of Corneal Epithelial Wound Closure. Appl Environ Microbiol 2020; 86:e00250-20. [PMID: 32414795 DOI: 10.1128/AEM.00250-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/08/2020] [Indexed: 12/17/2022] Open
Abstract
Tunable control of gene expression is an invaluable tool for biological experiments. In this study, we describe a new xylose-inducible promoter system and evaluate it in both Pseudomonas aeruginosa and Pseudomonas fluorescens The Pxut promoter, derived from the P. fluorescens xut operon, was incorporated into a broad-host-range pBBR1-based plasmid and was compared to the Escherichia coli-derived PBAD promoter using gfp as a reporter. Green fluorescent protein (GFP) fluorescence from the Pxut promoter was inducible in both Pseudomonas species, but not in E. coli, which may facilitate the cloning of genes toxic to E. coli to generate plasmids. The Pxut promoter was activated at a lower inducer concentration than PBAD in P. fluorescens, and higher gfp levels were achieved using Pxut Flow cytometry analysis indicated that Pxut was leakier than PBAD in the Pseudomonas species tested but was expressed in a higher proportion of cells when induced. d-Xylose as a sole carbon source did not support the growth of P. aeruginosa or P. fluorescens and is less expensive than many other commonly used inducers, which could facilitate large-scale applications. The efficacy of this system was demonstrated by its use to reveal a role for the P. aeruginosa type II secretion system gene xcpQ in bacterial inhibition of corneal epithelial cell wound closure. This study introduces a new inducible promoter system for gene expression for use in Pseudomonas species.IMPORTANCE Pseudomonas species are enormously important in human infections, in biotechnology, and as model systems for investigating basic science questions. In this study, we have developed a xylose-inducible promoter system, evaluated it in P. aeruginosa and P. fluorescens, and found it to be suitable for the strong induction of gene expression. Furthermore, we have demonstrated its efficacy in controlled gene expression to show that a type II secretion system protein from P. aeruginosa, XcpQ, is important for host-pathogen interactions in a corneal wound closure model.
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26
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Abstract
Design and implementation of synthetic biological circuits highly depends on well-characterized, robust promoters with predictable input-output responses. While great progress has been made with heterotrophic model organisms such as Escherichia coli, the available variety of tunable promoter parts for phototrophic cyanobacteria is still limited. Commonly used synthetic and semisynthetic promoters show weak dynamic ranges or no regulation at all in cyanobacterial models. Well-controlled alternatives such as native metal-responsive promoters, however, pose the problems of inducer toxicity and lacking orthogonality. Here, we present the comparative assessment of dose-response functions of four different inducible promoter systems in the model cyanobacterium Synechocystis sp. PCC 6803. Using the novel bimodular reporter plasmid pSHDY, dose-response dynamics of the re-established vanillate-inducible promoter PvanCC was compared to the previously described rhamnose-inducible Prha, the anhydrotetracycline-inducible PL03, and the Co2+-inducible PcoaT. We estimate individual advantages and disadvantages regarding dynamic range and strength of each promoter, also in comparison with well-established constitutive systems. We observed a delicate balance between transcription factor toxicity and sufficient expression to obtain a dose-dependent response to the inducer. In summary, we expand the current understanding and employability of inducible promoters in cyanobacteria, facilitating the scalability and robustness of synthetic regulatory network designs and of complex metabolic pathway engineering strategies.
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Affiliation(s)
- Anna Behle
- Institute for Synthetic Microbiology, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Pia Saake
- Institute for Synthetic Microbiology, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Anna T. Germann
- Institute for Synthetic Microbiology, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
| | - Dennis Dienst
- Department of Chemistry − Ångström, Uppsala University, 75120 Uppsala, Sweden
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany
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27
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Landberg J, Mundhada H, Nielsen AT. An autoinducible trp-T7 expression system for production of proteins and biochemicals in Escherichia coli. Biotechnol Bioeng 2020; 117:1513-1524. [PMID: 32022248 PMCID: PMC7186829 DOI: 10.1002/bit.27297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/11/2020] [Accepted: 02/03/2020] [Indexed: 12/19/2022]
Abstract
Inducible expression systems can be applied to control the expression of proteins or biochemical pathways in cell factories. However, several of the established systems require the addition of expensive inducers, making them unfeasible for large‐scale production. Here, we establish a genome integrated trp‐T7 expression system where tryptophan can be used to control the induction of a gene or a metabolic pathway. We show that the initiation of gene expression from low‐ and high‐copy vectors can be tuned by varying the initial concentration of tryptophan or yeast extract, and that expression is tightly regulated and homogenous when compared with the commonly used lac‐T7 system. Finally, we apply the trp‐T7 expression system for the production of l‐serine, where we reach titers of 26 g/L in fed‐batch fermentation.
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Affiliation(s)
- Jenny Landberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hemanshu Mundhada
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,CysBio ApS, Hørsholm, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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28
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Yang Y, Rong Z, Song H, Yang X, Li M, Yang S. Identification and characterization of ethanol- inducible promoters of Zymomonas mobilis based on omics data and dual reporter-gene system. Biotechnol Appl Biochem 2019; 67:158-165. [PMID: 31626362 DOI: 10.1002/bab.1838] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/13/2019] [Indexed: 12/22/2022]
Abstract
Zymomonas mobilis is a model bacterial ethanologen and has been engineered to produce lignocellulosic biofuels and biochemicals such as 2,3-butanediol. We have previously identified promoters of different strengths using systems biology datasets and characterized them using the flow cytometry-based dual reporter-gene system. Here, we further demonstrated the capability of applying the dual reporter-gene system and omics datasets on discovering inducible promoters. Ten candidate ethanol-inducible promoters were identified through omics datasets mining and clustering. Using the dual reporter-gene system, these promoters were characterized under natural growth, ethanol stress, and ethanol-induced condition to investigate the transcriptional strength and ethanol inducibility. The results demonstrated that three promoters of P0405, P0435, and P0038 driving the expression of native genes of ZMO0405, ZMO0435, and ZMO0038, correspondingly, are potential ethanol-responsive promoters and may be growth related. This study not only identified and verified three ethanol-inducible promoters as biological parts, which can be used to synchronize the expression of heterologous pathway genes with the ethanol production process of Z. mobilis, but also demonstrated the power of combining omics datasets and dual reporter-gene system to identify biological parts for metabolic engineering and synthetic biology applications in Z. mobilis and related microorganisms.
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Affiliation(s)
- Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Ziyue Rong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Haoyue Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Xiuxiu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., Ltd., Kaihua County, Zhejiang, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, China
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29
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Abstract
Recent synthetic biology efforts have raised biosafety concerns for possible release of engineered cyanobacteria into natural environments. To address the issues, we developed a controllable metal ion induced biocontainment system for two model cyanobacteria. First, six ion-inducible promoters were respectively evaluated in both Synechococcus elongatus PCC 7942 and the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973, leading to the identification of an iron ion-repressed promoter PisiAB with low leakage and a reduction-fold of 5.4 and 7.9, respectively. Second, holin-endolysin and nuclease NucA systems were introduced, the inhibition rate of which against two Synechococcus strains varied from 61% to 86.4%. Third, two toxin/antitoxin modules were identified capable of inducing programmed suicide in both Synechococcus strains after induction. Furthermore, an escape experiment was conducted and the results showed that the system was able to achieve an escape frequency below the detection limit of 10-9 after 3 days' duration, demonstrating the strategy integrating iron ion-inducible promoter PisiAB and that toxin/antitoxin modules could be a useful tool for cyanobacterium biocontainment.
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Affiliation(s)
- Yuqing Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072, P. R. China
| | | | - Zixi Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072, P. R. China
| | | | - Lei Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072, P. R. China
| | - Weiwen Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300072, P. R. China
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30
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Shin J, Kang S, Song Y, Jin S, Lee JS, Lee JK, Kim DR, Kim SC, Cho S, Cho BK. Genome Engineering of Eubacterium limosum Using Expanded Genetic Tools and the CRISPR-Cas9 System. ACS Synth Biol 2019; 8:2059-2068. [PMID: 31373788 DOI: 10.1021/acssynbio.9b00150] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Eubacterium limosum is one of the important bacteria in C1 feedstock utilization as well as in human gut microbiota. Although E. limosum has recently garnered much attention and investigation on a genome-wide scale, a bottleneck for systematic engineering in E. limosum is the lack of available genetic tools and an efficient genome editing platform. To overcome this limitation, we here report expanded genetic tools and the CRISPR-Cas9 system. We have developed an inducible promoter system that enables implementation of the CRISPR-Cas9 system to precisely manipulate target genes of the Wood-Ljungdahl pathway with 100% efficiency. Furthermore, we exploited the effectiveness of CRISPR interference to reduce the expression of target genes, exhibiting substantial repression of several genes in the Wood-Ljungdahl pathway and fructose-PTS system. These expanded genetic tools and CRISPR-Cas9 system comprise powerful and widely applicable genetic tools to accelerate functional genomic study and genome engineering in E. limosum.
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Affiliation(s)
- Jongoh Shin
- Department of Biological Sciences and KI for the BioCentury , KAIST , Daejeon , 305-701 , Republic of Korea
| | - Seulgi Kang
- Department of Biological Sciences and KI for the BioCentury , KAIST , Daejeon , 305-701 , Republic of Korea
| | - Yoseb Song
- Department of Biological Sciences and KI for the BioCentury , KAIST , Daejeon , 305-701 , Republic of Korea
| | - Sangrak Jin
- Department of Biological Sciences and KI for the BioCentury , KAIST , Daejeon , 305-701 , Republic of Korea
| | - Jin Soo Lee
- Department of Biological Sciences and KI for the BioCentury , KAIST , Daejeon , 305-701 , Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering , Konkuk University , Seoul , 05029 , Republic of Korea
| | - Dong Rip Kim
- Department of Mechanical Engineering , Hanyang University , Seoul , 04763 , Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences and KI for the BioCentury , KAIST , Daejeon , 305-701 , Republic of Korea
- Intelligent Synthetic Biology Center , Daejeon , 305-701 , Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury , KAIST , Daejeon , 305-701 , Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury , KAIST , Daejeon , 305-701 , Republic of Korea
- Intelligent Synthetic Biology Center , Daejeon , 305-701 , Republic of Korea
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31
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Zhou R, Comizzoli P, Keefer CL. Endogenous pluripotent factor expression after reprogramming cat fetal fibroblasts using inducible transcription factors. Mol Reprod Dev 2019; 86:1671-1681. [PMID: 31429169 DOI: 10.1002/mrd.23257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 07/29/2019] [Indexed: 02/05/2023]
Abstract
Incomplete transgene-silencing remains a challenge in the generation of induced pluripotent stem cells (iPSC) in felids-a critical family in biomedical and biodiversity conservation science. In this study doxycycline-inducible transgenes (NANOG, POU5F1, SOX2, KLF4, and cMYC) were used to reprogram cat fetal fibroblasts with the objective of obtaining iPSC with fully silenced transgenes. Colony formation was slower (14 vs. 8 days) and at lower efficiency than mouse embryonic fibroblasts (0.002% vs. 0.02% of seeded cells). Alkaline-phosphatase positive colonies were grown on feeder cells plus LIF and GSK3, MEK, and ROCK inhibitors. Cells could be passaged singly and transgene expression was silenced at passage 3 (P3) after doxycycline removal at P2. NANOG, POU5F1, and SOX2 were expressed at P3, P6, and P10, although at lower immunostaining intensities than in cat inner cell masses (ICM). Transcripts related to pluripotency (NANOG, POU5F1, SOX2, KLF4, cMYC, and REX1) and differentiation (FGF5, TBXT, GATA6, SOX17, FOXF1, PAX6, and SOX1) were assessed by a reverse transcription-quantitative polymerase chain reaction in iPSC and embryoid bodies. The immunostaining patterns, relatively low levels of NANOG and REX1 in comparison to ICM along with the expression of TBXT (mesoderm) suggested that cells were a mix of reprogrammed pluripotent and differentiating cells.
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Affiliation(s)
- Ran Zhou
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland.,Smithsonian Conservation Biology Institute (SCBI), National Zoological Park, Washington, DC
| | - Pierre Comizzoli
- Smithsonian Conservation Biology Institute (SCBI), National Zoological Park, Washington, DC
| | - Carol L Keefer
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland
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32
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Shi Q, Sutariya V, Varghese Gupta S, Bhatia D. GADD45α-targeted suicide gene therapy driven by synthetic CArG promoter E9NS sensitizes NSCLC cells to cisplatin, resveratrol, and radiation regardless of p53 status. Onco Targets Ther 2019; 12:3161-3170. [PMID: 31114253 PMCID: PMC6497884 DOI: 10.2147/ott.s192061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
Background: GADD45α is a tumor suppressor protein often upregulated by environmental stresses and DNA-damage agents to cause growth arrest, apoptosis, tumor growth inhibition, and anti-angiogenesis. A novel suicide gene therapy vector pE9NS.G45α was engineered by cloning GADD45α opening reading frame downstream to the synthetic CArG promoter E9NS, which contains nine repeats of CArG element with modified core A/T sequence and functions as a molecular switch to drive the expression of GADD45α. The current study aims to determine the efficacy of this suicide gene therapy vector in combination with cisplatin, resveratrol, and radiation in NSCLC cell lines with various p53 statuses. Methods: Three NSCLC cell lines, H1299 (deleted p53), A549 (wild-type p53), and H23 (mutated p53), were examined in the present investigation to represent NSCLC with different p53 functions. MTT assay was conducted to select suitable doses of cisplatin, resveratrol, and radiation for gene therapy, and dual luciferase assay was performed to validate the activation of promoter E9NS. The efficacy of gene therapy combinations was evaluated by the amount of GADD45α expression, cell survival, and apoptosis. Results: All the combinations successfully activated promoter E9NS to elevate intracellular GADD45α protein levels and subsequently enhanced cell viability reduction and apoptosis induction regardless of p53 status. Conclusion: Our study demonstrates that GADD45α-targeted suicide gene therapy controlled by synthetic promoter E9NS sensitizes NSCLC cells to cisplatin, resveratrol, and radiation and is effective against NSCLC at least in vitro.
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Affiliation(s)
- Qiwen Shi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | | | | | - Deepak Bhatia
- Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, VA, USA
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Arnaiz A, Martinez M, Gonzalez-Melendi P, Grbic V, Diaz I, Santamaria ME. Plant Defenses Against Pests Driven by a Bidirectional Promoter. Front Plant Sci 2019; 10:930. [PMID: 31379907 PMCID: PMC6652247 DOI: 10.3389/fpls.2019.00930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/02/2019] [Indexed: 05/06/2023]
Abstract
The plant defense responses to pests results in the synchronized change of a complex network of interconnected genes and signaling pathways. An essential part of this process is mediated by the binding of transcription factors to the specific responsive cis-elements within in the promoters of phytophagous-responsive genes. In this work, it is reported the identification and characterization of a bidirectional promoter that simultaneously co-regulate two divergent genes, At5g10300 and At5g10290, upon arthropod feeding. Computational analysis identified the presence of cis-elements within the intergenic region between two loci, mainly from the DOF but also from the AP2/ERF, Golden 2-like and bHLH families. The function of the bidirectional promoter was analyzed using two enhanced variants of the GFP and CherryFP reporter genes, in both orientations, in transient tobacco and stably transformed Arabidopsis plants. Promoter activity was tested in response to feeding of Tetranychus urticae and Pieris brassicae, as well as wounding, flagellin and chitin treatments. Using RT-qPCR assays and confocal microscopy, it was shown that all treatments resulted in the induction of both reporter genes. Furthermore, our findings revealed the asymmetric character of the promoter with stronger activity in the forward than in the reverse orientation. This study provides an example of a bidirectional promoter with a strong potential to be used in plant biotechnology in pest control that requires stacking of the defense genes.
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Affiliation(s)
- Ana Arnaiz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Pablo Gonzalez-Melendi
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Vojislava Grbic
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - M. Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: M. Estrella Santamaria,
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Kumar N, Stanford W, de Solis C, Aradhana, Abraham ND, Dao TMJ, Thaseen S, Sairavi A, Gonzalez CU, Ploski JE. The Development of an AAV-Based CRISPR SaCas9 Genome Editing System That Can Be Delivered to Neurons in vivo and Regulated via Doxycycline and Cre-Recombinase. Front Mol Neurosci 2018; 11:413. [PMID: 30483052 PMCID: PMC6243075 DOI: 10.3389/fnmol.2018.00413] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/24/2018] [Indexed: 11/13/2022] Open
Abstract
The RNA-guided Cas9 nuclease, from the type II prokaryotic clustered regularly interspersed short palindromic repeats (CRISPR) adaptive immune system, has been adapted by scientists to enable site specific genome editing of eukaryotic cells both in vitro and in vivo. Previously, we reported the development of an adeno-associated virus (AAV)-mediated CRISPR Streptococcus pyogenes (Sp) Cas9 system, in which the genome editing function can be regulated by controlling the expression of the guide RNA (sgRNA) in a doxycycline (Dox)-dependent manner. Here, we report the development of an AAV vector tool kit utilizing the Cas9 from Staphylococcus aureus (SaCas9). We demonstrate in vitro genome editing in human derived 293FT cells and mouse derived Neuro2A (N2A) cells and in vivo in neurons of the mouse brain. We also demonstrate the ability to regulate the induction of genome editing temporally with Dox and spatially with Cre-recombinase. The combination of these systems enables AAV-mediated CRISPR/Cas9 genome editing to be regulated both spatially and temporally.
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Affiliation(s)
- Namrata Kumar
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - William Stanford
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - Christopher de Solis
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - Aradhana
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - Nigel D Abraham
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - Trieu-Mi J Dao
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - Sadiqa Thaseen
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - Anusha Sairavi
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - Cuauhtemoc Ulises Gonzalez
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
| | - Jonathan E Ploski
- School of Behavioral and Brain Sciences, Department of Molecular & Cell Biology, The University of Texas at Dallas, Richardson, TX, United States
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Fitz E, Wanka F, Seiboth B. The Promoter Toolbox for Recombinant Gene Expression in Trichoderma reesei. Front Bioeng Biotechnol 2018; 6:135. [PMID: 30364340 PMCID: PMC6193071 DOI: 10.3389/fbioe.2018.00135] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/12/2018] [Indexed: 01/05/2023] Open
Abstract
The ascomycete Trichoderma reesei is one of the main fungal producers of cellulases and xylanases based on its high production capacity. Its enzymes are applied in food, feed, and textile industry or in lignocellulose hydrolysis in biofuel and biorefinery industry. Over the last years, the demand to expand the molecular toolbox for T. reesei to facilitate genetic engineering and improve the production of heterologous proteins grew. An important instrument to modify the expression of key genes are promoters to initiate and control their transcription. To date, the most commonly used promoter for T. reesei is the strong inducible promoter of the main cellobiohydrolase cel7a. Beside this one, there is a number of alternative inducible promoters derived from other cellulase- and xylanase encoding genes and a few constitutive promoters. With the advances in genomics and transcriptomics the identification of new constitutive and tunable promoters with different expression strength was simplified. In this review, we will discuss new developments in the field of promoters and compare their advantages and disadvantages. Synthetic expression systems constitute a new option to control gene expression and build up complex gene circuits. Therefore, we will address common structural features of promoters and describe options for promoter engineering and synthetic design of promoters. The availability of well-characterized gene expression control tools is essential for the analysis of gene function, detection of bottlenecks in gene networks and yield increase for biotechnology applications.
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Affiliation(s)
- Elisabeth Fitz
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Franziska Wanka
- Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB) GmbH, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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Abstract
Synthetic biology is rapidly evolving into a new phase that emphasizes real-world applications such as environmental remediation. Recently, Comamonas testosteroni has become a promising chassis for bioremediation due to its natural pollutant-degrading capacity; however, its application is hindered by the lack of fundamental gene expression tools. Here, we present a synthetic biology toolkit that enables rapid creation of functional gene circuits in C. testosteroni. We first built a shuttle system that allows efficient circuit construction in E. coli and necessary phenotypic testing in C. testosteroni. Then, we tested a set of wildtype inducible promoters, and further used a hybrid strategy to create engineered promoters to expand expression strength and dynamics. Additionally, we tested the T7 RNA Polymerase-PT7 promoter system and reduced its leaky expression through promoter mutation for gene expression. By coupling random library construction with FACS screening, we further developed a synthetic T7 promoter library to confer a wider range of expression strength and dynamic characteristics. This study provides a set of valuable tools to engineer gene circuits in C. testosteroni, facilitating the establishment of the organism as a useful microbial chassis for bioremediation purposes.
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Affiliation(s)
- Qiang Tang
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Environmental Microbiology Research Center, Chinese Academy of Sciences, Beijing 100101, China
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37
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Huang TK, Falk BW, Dandekar AM, McDonald KA. Enhancement of Recombinant Protein Production in Transgenic Nicotiana benthamiana Plant Cell Suspension Cultures with Co-Cultivation of Agrobacterium Containing Silencing Suppressors. Int J Mol Sci 2018; 19:E1561. [PMID: 29882931 PMCID: PMC6032394 DOI: 10.3390/ijms19061561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/06/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
We have previously demonstrated that the inducible plant viral vector (CMViva) in transgenic plant cell cultures can significantly improve the productivity of extracellular functional recombinant human alpha-1-antiryspin (rAAT) compared with either a common plant constitutive promoter (Cauliflower mosaic virus (CaMV) 35S) or a chemically inducible promoter (estrogen receptor-based XVE) system. For a transgenic plant host system, however, viral or transgene-induced post-transcriptional gene silencing (PTGS) has been identified as a host response mechanism that may dramatically reduce the expression of a foreign gene. Previous studies have suggested that viral gene silencing suppressors encoded by a virus can block or interfere with the pathways of transgene-induced PTGS in plant cells. In this study, the capability of nine different viral gene silencing suppressors were evaluated for improving the production of rAAT protein in transgenic plant cell cultures (CMViva, XVE or 35S system) using an Agrobacterium-mediated transient expression co-cultivation process in which transgenic plant cells and recombinant Agrobacterium carrying the viral gene silencing suppressor were grown together in suspension cultures. Through the co-cultivation process, the impacts of gene silencing suppressors on the rAAT production were elucidated, and promising gene silencing suppressors were identified. Furthermore, the combinations of gene silencing suppressors were optimized using design of experiments methodology. The results have shown that in transgenic CMViva cell cultures, the functional rAAT as a percentage of total soluble protein is increased 5.7 fold with the expression of P19, and 17.2 fold with the co-expression of CP, P19 and P24.
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Affiliation(s)
- Ting-Kuo Huang
- Department of Chemical Engineering and Materials Science, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
| | - Bryce W Falk
- Department of Plant Pathology, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
| | - Karen A McDonald
- Department of Chemical Engineering and Materials Science, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
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38
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Gabner S, Ertl R, Velde K, Renner M, Jenner F, Egerbacher M, Hlavaty J. Cytokine-induced interleukin-1 receptor antagonist protein expression in genetically engineered equine mesenchymal stem cells for osteoarthritis treatment. J Gene Med 2018; 20:e3021. [PMID: 29608232 PMCID: PMC6001542 DOI: 10.1002/jgm.3021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/23/2018] [Accepted: 03/24/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A combination of tissue engineering methods employing mesenchymal stem cells (MSCs) together with gene transfer takes advantage of innovative strategies and highlights a new approach for targeting osteoarthritis (OA) and other cartilage defects. Furthermore, the development of systems allowing tunable transgene expression as regulated by natural disease-induced substances is highly desirable. METHODS Bone marrow-derived equine MSCs were transduced with a lentiviral vector expressing interleukin-1 receptor antagonist (IL-1Ra) gene under the control of an inducible nuclear factor-kappa B-responsive promoter and IL-1Ra production upon pro-inflammatory cytokine stimulation [tumor necrosis factor (TNF)α, interleukin (IL)-1β] was analysed. To assess the biological activity of the IL-1Ra protein that was produced and the therapeutic effect of IL-1Ra-expressing MSCs (MSC/IL-1Ra), cytokine-based two- and three-dimensional in vitro models of osteoarthritis using equine chondrocytes were established and quantitative real-time polymerase chain reaction (PCR) analysis was used to measure the gene expression of aggrecan, collagen IIA1, interleukin-1β, interleukin-6, interleukin-8, matrix metalloproteinase-1 and matrix metalloproteinase-13. RESULTS A dose-dependent increase in IL-1Ra expression was found in MSC/IL-1Ra cells upon TNFα administration, whereas stimulation using IL-1β did not lead to IL-1Ra production above the basal level observed in nonstimulated cells as a result of the existing feedback loop. Repeated cycles of induction allowed on/off modulation of transgene expression. In vitro analyses revealed that IL-1Ra protein present in the conditioned medium from MSC/IL-1Ra cells blocks OA onset in cytokine-treated equine chondrocytes and co-cultivation of MSC/IL-1Ra cells with osteoarthritic spheroids alleviates the severity of the osteoarthritic changes. CONCLUSIONS Thus, pro-inflammatory cytokine induced IL-1Ra protein expression from genetically modified MSCs might represent a promising strategy for osteoarthritis treatment.
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Affiliation(s)
- Simone Gabner
- Institute of Pathology and Forensic Veterinary Medicine, Working Group Histology and EmbryologyUniversity of Veterinary Medicine ViennaViennaAustria
| | - Reinhard Ertl
- VetCORE, Facility for ResearchUniversity of Veterinary MedicineViennaAustria
| | - Karsten Velde
- Equine University HospitalUniversity of Veterinary Medicine ViennaViennaAustria
| | - Matthias Renner
- Division of Medical BiotechnologyPaul‐Ehrlich‐InstitutLangenGermany
| | - Florien Jenner
- Equine University HospitalUniversity of Veterinary Medicine ViennaViennaAustria
| | - Monika Egerbacher
- Institute of Pathology and Forensic Veterinary Medicine, Working Group Histology and EmbryologyUniversity of Veterinary Medicine ViennaViennaAustria
| | - Juraj Hlavaty
- Institute of Pathology and Forensic Veterinary Medicine, Working Group Histology and EmbryologyUniversity of Veterinary Medicine ViennaViennaAustria
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Kelly CL, Taylor GM, Hitchcock A, Torres-Méndez A, Heap JT. A Rhamnose-Inducible System for Precise and Temporal Control of Gene Expression in Cyanobacteria. ACS Synth Biol 2018; 7:1056-1066. [PMID: 29544054 DOI: 10.1021/acssynbio.7b00435] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyanobacteria are important for fundamental studies of photosynthesis and have great biotechnological potential. In order to better study and fully exploit these organisms, the limited repertoire of genetic tools and parts must be expanded. A small number of inducible promoters have been used in cyanobacteria, allowing dynamic external control of gene expression through the addition of specific inducer molecules. However, the inducible promoters used to date suffer from various drawbacks including toxicity of inducers, leaky expression in the absence of inducer and inducer photolability, the latter being particularly relevant to cyanobacteria, which, as photoautotrophs, are grown under light. Here we introduce the rhamnose-inducible rhaBAD promoter of Escherichia coli into the model freshwater cyanobacterium Synechocystis sp. PCC 6803 and demonstrate it has superior properties to previously reported cyanobacterial inducible promoter systems, such as a non-toxic, photostable, non-metabolizable inducer, a linear response to inducer concentration and crucially no basal transcription in the absence of inducer.
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Affiliation(s)
- Ciarán L. Kelly
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - George M. Taylor
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Andrew Hitchcock
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Antonio Torres-Méndez
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - John T. Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
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Li S, Wang J, Xiang W, Yang K, Li Z, Wang W. An Autoregulated Fine-Tuning Strategy for Titer Improvement of Secondary Metabolites Using Native Promoters in Streptomyces. ACS Synth Biol 2018; 7:522-530. [PMID: 29087698 DOI: 10.1021/acssynbio.7b00318] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Streptomycetes are well-known producers of biologically active secondary metabolites. Various efforts have been made to increase productions of these metabolites, while few approaches could well coordinate the biosynthesis of secondary metabolites and other physiological events of their hosts. Here we develop a universal autoregulated strategy for fine-tuning the expression of secondary metabolites biosynthetic gene clusters (BGCs) in Streptomyces species. First, inducible promoters were used to control the expression of secondary metabolites BGCs. Then, the optimal induction condition was determined by response surface model in both dimensions of time and strength. Finally, native promoters with similar transcription profile to the inducible promoter under the optimal condition were identified based on time-course transcriptome analyses, and used to replace the inducible promoter following an elaborate replacement approach. The expression of actinorhodin (Act) and heterogeneous oxytetracycline (OTC) BGCs were optimized in Streptomyces coelicolor using this strategy. Compared to modulating the expression via constitutive promoters, our strategy could dramatically improve the titers of Act and OTC by 1.3- and 9.1-fold, respectively. The autoregulated fine-tuning strategy developed here opens a novel route for titer improvement of desired secondary metabolites in Streptomyces.
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Affiliation(s)
- Shanshan Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute
of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District,
Beijing 100193, China
| | - Junyang Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Wensheng Xiang
- State
Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute
of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian District,
Beijing 100193, China
| | - Keqian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Zilong Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Weishan Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, China
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Gabner S, Hlavaty J, Velde K, Renner M, Jenner F, Egerbacher M. Inflammation-induced transgene expression in genetically engineered equine mesenchymal stem cells. J Gene Med 2018; 18:154-64. [PMID: 27272202 DOI: 10.1002/jgm.2888] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Osteoarthritis, a chronic and progressive degenerative joint disorder, ranks amongst the top five causes of disability. Given the high incidence, associated socioeconomic costs and the absence of effective disease-modifying therapies of osteoarthritis, cell-based treatments offer a promising new approach. Owing to their paracrine, differentiation and self-renewal abilities, mesenchymal stem cells (MSCs) have great potential for regenerative medicine, which might be further enhanced by targeted gene therapy. Hence, the development of systems allowing transgene expression, particularly when regulated by natural disease-dependent occuring substances, is of high interest. METHODS Bone marrow-isolated equine MSCs were stably transduced with an HIV-1 based lentiviral vector expressing the luciferase gene under control of an inducible nuclear factor κB (NFκB)-responsive promoter. Marker gene expression was analysed by determining luciferase activity in transduced cells stimulated with different concentrations of interleukin (IL)-1β or tumour necrosis factor (TNF)α. RESULTS A dose-dependent increase in luciferase expression was observed in transduced MSCs upon cytokine stimulation. The induction effect was more potent in cells treated with TNFα compared to those treated with IL-1β. Maximum transgene expression was obtained after 48 h of stimulation and the same time was necessary to return to baseline luciferase expression levels after withdrawal of the stimulus. Repeated cycles of induction allowed on-off modulation of transgene expression without becoming refractory to induction. The NFκB-responsive promoter retained its inducibility also in chondrogenically differentiated MSC/Luc cells. CONCLUSIONS The results of the present study demonstrate that on demand transgene expression from the NFκB-responsive promoter using naturally occurring inflammatory cytokines can be induced in undifferentiated and chondrogenically differentiated equine MSCs. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Simone Gabner
- Institute of Anatomy, Histology and Embryology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Juraj Hlavaty
- Institute of Anatomy, Histology and Embryology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Karsten Velde
- Equine University Hospital, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Matthias Renner
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Florien Jenner
- Equine University Hospital, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Monika Egerbacher
- Institute of Anatomy, Histology and Embryology, University of Veterinary Medicine Vienna, Vienna, Austria
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Magaña Vergara C, Kallenberg CJL, Rogasch M, Hübner CG, Song Y. A versatile vector for mycobacterial protein production with a functional minimized acetamidase regulon. Protein Sci 2017; 26:2302-2311. [PMID: 28857325 PMCID: PMC5654848 DOI: 10.1002/pro.3288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 06/09/2017] [Accepted: 08/22/2017] [Indexed: 11/10/2022]
Abstract
Recombinant protein expression is a prerequisite for diverse investigations of proteins at the molecular level. For targets from Mycobacterium tuberculosis it is favorable to use M. smegmatis as an expression host, a species from the same genus. In the respective shuttle vectors, target gene expression is controlled by the complex tetra-cistronic acetamidase regulon. As a result, the size of those vectors is large, rendering them of limited use, especially when the target proteins are expressed from multi-cistronic operons. Therefore, in the current work we present a versatile new expression vector in which the acetamidase regulon has been minimized by deleting the two genes amiD and amiS. We assessed the functional properties of the resulting vector pMyCA and compared it with those of the existing vector pMyNT that contains the full-length acetamidase regulon. We analyzed the growth features and protein expression patterns of M. smegmatis cultures transformed with both vectors. In addition, we created mCherry expression constructs to spectroscopically monitor the expression properties of both vectors. Our experiments showed that the minimized vector exhibited several advantages over the pMyNT vector. First, the overall yield of expressed protein is higher due to the higher yield of bacterial mass. Second, the heterologous expression was regulated more tightly, offering an expression tool for diverse target proteins. Third, it is suitable for large multi-protein complexes that are expressed from multi-cistronic operons. Additionally, our results propose a new understanding of the regulation mechanism of the acetamidase regulon with the potential to construct more optimized vectors in the future.
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Affiliation(s)
| | | | - Miriam Rogasch
- Institute of Physics, University of Luebeck, Ratzeburger Allee 160Luebeck23562Germany
| | | | - Young‐Hwa Song
- Institute of Physics, University of Luebeck, Ratzeburger Allee 160Luebeck23562Germany
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Zhang H, Jing R, Mao X. Functional Characterization of TaSnRK2.8 Promoter in Response to Abiotic Stresses by Deletion Analysis in Transgenic Arabidopsis. Front Plant Sci 2017; 8:1198. [PMID: 28751901 PMCID: PMC5507967 DOI: 10.3389/fpls.2017.01198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
Drought, salinity, and cold are the major factors limiting wheat quality and productivity; it is thus highly desirable to characterize the abiotic-stress-inducible promoters suitable for the genetic improvement of plant resistance. The sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family genes show distinct regulatory properties in response to abiotic stresses. The present study characterized the approximately 3000-bp upstream sequence (the 313 bp upstream of the ATG was the transcription start site) of the Triticum aestivum TaSnRK2.8 promoter under abscisic acid (ABA) and abiotic stresses. Four different-length 5' deletion fragments of TaSnRK2.8 promoter were fused with the GUS reporter gene and transformed into Arabidopsis. Tissue expression analysis showed that the TaSnRK2.8 promoter region from position -1481 to -821 contained the stalk-specific elements, and the region from position -2631 to -1481 contained the leaf- and root-specific elements. In the ABA-treated seedlings, the deletion analysis showed that the TaSnRK2.8 promoter region from position -821 to -2631 contained ABA response elements. The abiotic stress responses of the TaSnRK2.8 promoter derivatives demonstrated that they harbored abiotic-stress response elements: the region from position -821 to -408 harbored the osmotic-stress response elements, whereas the region from position -2631 to -1481 contained the positive regulatory motifs and the region from position -1481 to -821 contained the leaf- and stalk-specific enhancers. Further deletion analysis of the promoter region from position -821 to -408 indicated that a 125-bp region from position -693 to -568 was required to induce an osmotic-stress response. These results contribute to a better understanding of the molecular mechanisms of TaSnRK2.8 in response to abiotic stresses, and the TaSnRK2.8 promoter seems to be a candidate for regulating the expression of abiotic stress response genes in transgenic plants.
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Affiliation(s)
- Hongying Zhang
- College of Tobacco Science, Henan Agricultural UniversityZhengzhou, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Ruilian Jing
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xinguo Mao
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
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44
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Ohira MJ, Hendrickson DG, Scott McIsaac R, Rhind N. An estradiol- inducible promoter enables fast, graduated control of gene expression in fission yeast. Yeast 2017; 34:323-334. [PMID: 28423198 DOI: 10.1002/yea.3235] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 11/09/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe lacks a diverse toolkit of inducible promoters for experimental manipulation. Available inducible promoters suffer from slow induction kinetics, limited control of expression levels and/or a requirement for defined growth medium. In particular, no S. pombe inducible promoter systems exhibit a linear dose-response, which would allow expression to be tuned to specific levels. We have adapted a fast, orthogonal promoter system with a large dynamic range and a linear dose response, based on β-estradiol-regulated function of the human oestrogen receptor, for use in S. pombe. We show that this promoter system, termed Z3 EV, turns on quickly, can reach a maximal induction of 20-fold, and exhibits a linear dose response over its entire induction range, with few off-target effects. We demonstrate the utility of this system by regulating the mitotic inhibitor Wee1 to create a strain in which cell size is regulated by β-estradiol concentration. This promoter system will be of great utility for experimentally regulating gene expression in fission yeast. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Makoto J Ohira
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA
| | - David G Hendrickson
- Calico Life Sciences, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - R Scott McIsaac
- Calico Life Sciences, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Nicholas Rhind
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA
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45
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Lim B, Zimmermann M, Barry NA, Goodman AL. Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut. Cell 2017; 169:547-558.e15. [PMID: 28431252 PMCID: PMC5532740 DOI: 10.1016/j.cell.2017.03.045] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/28/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022]
Abstract
The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution of microbiome gene products to community assembly, host physiology, and disease. We developed a panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer. In the absence of inducer, promoter activity is fully repressed; addition of inducer rapidly increases gene expression by four to five orders of magnitude. Because the inducer is absent in mice and their diets, Bacteroides gene expression inside the gut can be modulated by providing the inducer in drinking water. We use this system to measure the dynamic relationship between commensal sialidase activity and liberation of mucosal sialic acid, a receptor and nutrient for pathogens. VIDEO ABSTRACT.
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Affiliation(s)
- Bentley Lim
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536-0812, USA
| | - Michael Zimmermann
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536-0812, USA
| | - Natasha A Barry
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536-0812, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06536-0812, USA.
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46
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Kelly CL, Liu Z, Yoshihara A, Jenkinson SF, Wormald MR, Otero J, Estévez A, Kato A, Marqvorsen MHS, Fleet GWJ, Estévez RJ, Izumori K, Heap JT. Synthetic Chemical Inducers and Genetic Decoupling Enable Orthogonal Control of the rhaBAD Promoter. ACS Synth Biol 2016; 5:1136-1145. [PMID: 27247275 DOI: 10.1021/acssynbio.6b00030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
External control of gene expression is crucial in synthetic biology and biotechnology research and applications, and is commonly achieved using inducible promoter systems. The E. coli rhamnose-inducible rhaBAD promoter has properties superior to more commonly used inducible expression systems, but is marred by transient expression caused by degradation of the native inducer, l-rhamnose. To address this problem, 35 analogues of l-rhamnose were screened for induction of the rhaBAD promoter, but no strong inducers were identified. In the native configuration, an inducer must bind and activate two transcriptional activators, RhaR and RhaS. Therefore, the expression system was reconfigured to decouple the rhaBAD promoter from the native rhaSR regulatory cascade so that candidate inducers need only activate the terminal transcription factor RhaS. Rescreening the 35 compounds using the modified rhaBAD expression system revealed several promising inducers. These were characterized further to determine the strength, kinetics, and concentration-dependence of induction; whether the inducer was used as a carbon source by E. coli; and the modality (distribution) of induction among populations of cells. l-Mannose was found to be the most useful orthogonal inducer, providing an even greater range of induction than the native inducer l-rhamnose, and crucially, allowing sustained induction instead of transient induction. These findings address the key limitation of the rhaBAD expression system and suggest it may now be the most suitable system for many applications.
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Affiliation(s)
- Ciarán L. Kelly
- Centre
for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
| | - Zilei Liu
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Akihide Yoshihara
- International
Institute of Rare Sugar Research and Education, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Sarah F. Jenkinson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Mark R. Wormald
- Glycobiology
Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, U.K
| | - Jose Otero
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Amalia Estévez
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Atsushi Kato
- Department
of Hospital Pharmacy, University of Toyama, Toyama 930-0194, Japan
| | - Mikkel H. S. Marqvorsen
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - George W. J. Fleet
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K
| | - Ramón J. Estévez
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Ken Izumori
- International
Institute of Rare Sugar Research and Education, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - John T. Heap
- Centre
for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
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Horn N, Carvalho AL, Overweg K, Wegmann U, Carding SR, Stentz R. A Novel Tightly Regulated Gene Expression System for the Human Intestinal Symbiont Bacteroides thetaiotaomicron. Front Microbiol 2016; 7:1080. [PMID: 27468280 PMCID: PMC4942465 DOI: 10.3389/fmicb.2016.01080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
There is considerable interest in studying the function of Bacteroides species resident in the human gastrointestinal (GI)-tract and the contribution they make to host health. Reverse genetics and protein expression techniques, such as those developed for well-characterized Escherichia coli cannot be applied to Bacteroides species as they and other members of the Bacteriodetes phylum have unique promoter structures. The availability of useful Bacteroides-specific genetic tools is therefore limited. Here we describe the development of an effective mannan-controlled gene expression system for Bacteroides thetaiotaomicron containing the mannan-inducible promoter-region of an α-1,2-mannosidase gene (BT_3784), a ribosomal binding site designed to modulate expression, a multiple cloning site to facilitate the cloning of genes of interest, and a transcriptional terminator. Using the Lactobacillus pepI as a reporter gene, mannan induction resulted in an increase of reporter activity in a time- and concentration-dependent manner with a wide range of activity. The endogenous BtcepA cephalosporinase gene was used to demonstrate the suitability of this novel expression system, enabling the isolation of a His-tagged version of BtCepA. We have also shown with experiments performed in mice that the system can be induced in vivo in the presence of an exogenous source of mannan. By enabling the controlled expression of endogenous and exogenous genes in B. thetaiotaomicron this novel inducer-dependent expression system will aid in defining the physiological role of individual genes and the functional analyses of their products.
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Affiliation(s)
- Nikki Horn
- Gut Health and Food Safety Programme, Carding's Lab, Institute of Food Research Norwich, UK
| | - Ana L Carvalho
- Gut Health and Food Safety Programme, Carding's Lab, Institute of Food Research Norwich, UK
| | - Karin Overweg
- Gut Health and Food Safety Programme, Carding's Lab, Institute of Food Research Norwich, UK
| | - Udo Wegmann
- Gut Health and Food Safety Programme, Carding's Lab, Institute of Food Research Norwich, UK
| | - Simon R Carding
- Gut Health and Food Safety Programme, Carding's Lab, Institute of Food ResearchNorwich, UK; Department of Medicine, Norwich Medical School, University of East AngliaNorwich, UK
| | - Régis Stentz
- Gut Health and Food Safety Programme, Carding's Lab, Institute of Food Research Norwich, UK
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Abstract
The Bacillus subtilis 168 genome is being used to clone DNA segments, particularly unmarked DNA segments between the two available clones. To facilitate this cloning, a counter selection method was developed in which loss of a cI repressor gene rendered the host strain resistant to neomycin. This method is promoted to use the B. subtilis genome as a general cloning vehicle.
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49
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Zhang H, Hou J, Jiang P, Qi S, Xu C, He Q, Ding Z, Wang Z, Zhang K, Li K. Identification of a 467 bp Promoter of Maize Phosphatidylinositol Synthase Gene (ZmPIS) Which Confers High-Level Gene Expression and Salinity or Osmotic Stress Inducibility in Transgenic Tobacco. Front Plant Sci 2016; 7:42. [PMID: 26870063 PMCID: PMC4740949 DOI: 10.3389/fpls.2016.00042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/11/2016] [Indexed: 05/03/2023]
Abstract
Salinity and drought often affect plant growth and crop yields. Cloning and identification of salinity and drought stress inducible promoters is of great significance for their use in the genetic improvement of crop resistance. Previous studies showed that phosphatidylinositol synthase is involved in plant salinity and drought stress responses but its promoter has not been characterized by far. In the study, the promoter (pZmPIS, 1834 bp upstream region of the translation initiation site) was isolated from maize genome. To functionally validate the promoter, eight 5' deletion fragments of pZmPIS in different lengths were fused to GUS to produce pZmPIS::GUS constructs and transformed into tobacco, namely PZ1-PZ8. The transcription activity and expression pattern obviously changed when the promoter was truncated. Previous studies have demonstrated that NaCl and PEG treatments are usually used to simulate salinity and drought treatments. The results showed that PZ1-PZ7 can respond well upon NaCl and PEG treatments, while PZ8 not. PZ7 (467 bp) displayed the highest transcription activity in all tissues of transgenic tobacco amongst 5' deleted promoter fragments, which corresponds to about 20 and 50% of CaMV35S under normal and NaCl or PEG treatment, respectively. This implied that PZ7 is the core region of pZmPIS which confers high-level gene expression and NaCl or PEG inducible nature. The 113 bp segment between PZ7 and PZ8 (-467 to -355 bp) was considered as the key sequence for ZmPIS responding to NaCl or PEG treatment. GUS transient assay in tobacco leaves showed that this segment was sufficient for the NaCl or PEG stress response. Bioinformatic analysis revealed that the 113 bp sequence may contain new elements that are crucial for ZmPIS response to NaCl or PEG stress. These results promote our understanding on transcriptional regulation mechanism of ZmPIS and the characterized PZ7 promoter fragment would be an ideal candidate for the overexpression of drought and salinity responsive gene to improve crop resistance.
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Affiliation(s)
- Hongli Zhang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong UniversityJinan, China
| | - Jiajia Hou
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong UniversityJinan, China
| | - Pingping Jiang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong UniversityJinan, China
| | - Shoumei Qi
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong UniversityJinan, China
| | - Changzheng Xu
- Research Center of Bioenergy and Bioremediation, College of Resources and Environment, Southwest UniversityChongqing, China
| | - Qiuxia He
- Biology Institute of Shandong Academy of SciencesJinan, China
| | - Zhaohua Ding
- Maize Institute of Shandong Academy of Agricultural SciencesJinan, China
| | - Zhiwu Wang
- Maize Institute of Shandong Academy of Agricultural SciencesJinan, China
| | - Kewei Zhang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong UniversityJinan, China
| | - Kunpeng Li
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong UniversityJinan, China
- *Correspondence: Kunpeng Li,
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50
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Corbin JM, Hashimoto BI, Karuppanan K, Kyser ZR, Wu L, Roberts BA, Noe AR, Rodriguez RL, McDonald KA, Nandi S. Semicontinuous Bioreactor Production of Recombinant Butyrylcholinesterase in Transgenic Rice Cell Suspension Cultures. Front Plant Sci 2016; 7:412. [PMID: 27066048 PMCID: PMC4814504 DOI: 10.3389/fpls.2016.00412] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 03/17/2016] [Indexed: 05/17/2023]
Abstract
An active and tetrameric form of recombinant butyrylcholinesterase (BChE), a large and complex human enzyme, was produced via semicontinuous operation in a transgenic rice cell suspension culture. After transformation of rice callus and screening of transformants, the cultures were scaled up from culture flask to a lab scale bioreactor. The bioreactor was operated through two phases each of growth and expression. The cells were able to produce BChE during both expression phases, with a maximum yield of 1.6 mg BChE/L of culture during the second expression phase. Cells successfully regrew during a 5-day growth phase. A combination of activity assays and Western blot analysis indicated production of an active and fully assembled tetramer of BChE.
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Affiliation(s)
- Jasmine M. Corbin
- Chemical Engineering and Materials Science, University of California, DavisDavis, CA, USA
| | - Bryce I. Hashimoto
- Chemical Engineering and Materials Science, University of California, DavisDavis, CA, USA
| | - Kalimuthu Karuppanan
- Chemical Engineering and Materials Science, University of California, DavisDavis, CA, USA
| | - Zachary R. Kyser
- Chemical Engineering and Materials Science, University of California, DavisDavis, CA, USA
| | | | | | | | - Raymond L. Rodriguez
- Global HealthShare®, Molecular and Cellular Biology, University of California, DavisDavis, CA, USA
| | - Karen A. McDonald
- Chemical Engineering and Materials Science, University of California, DavisDavis, CA, USA
| | - Somen Nandi
- Global HealthShare®, Molecular and Cellular Biology, University of California, DavisDavis, CA, USA
- *Correspondence: Somen Nandi
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