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Han L, Chen Q, Lin Q, Cheng J, Zhou L, Liu Z, Guo J, Zhang L, Cui W, Zhou Z. Realization of Robust and Precise Regulation of Gene Expression by Multiple Sigma Recognizable Artificial Promoters. Front Bioeng Biotechnol 2020; 8:92. [PMID: 32140461 PMCID: PMC7042180 DOI: 10.3389/fbioe.2020.00092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/31/2020] [Indexed: 01/28/2023] Open
Abstract
Precise regulation of gene expression is fundamental for tailor-made gene circuit design in synthetic biology. Current strategies for this type of development are mainly based on directed evolution beginning with a native promoter template. The performances of engineered promoters are usually limited by the growth phase because only one promoter is recognized by one type of sigma factor (σ). Here, we constructed multiple-σ recognizable artificial hybrid promoters (AHPs) composed of tandems of dual and triple natural minimal promoters (NMPs). These NMPs, which use σA, σH and σW, had stable functions in different growth phases. The functions of these NMPs resulted from an effect called transcription compensation, in which AHPs sequentially use one type of σ in the corresponding growth phase. The strength of the AHPs was influenced by the combinatorial order of each NMP and the length of the spacers between the NMPs. More importantly, the output of the precise regulation was achieved by equipping AHPs with synthetic ribosome binding sites and by redesigning them for induced systems. This strategy might offer promising applications to rationally design robust synthetic promoters in diverse chassis to spur the construction of more complex gene circuits, which will further the development of synthetic biology.
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Affiliation(s)
- Laichuang Han
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiaoqing Chen
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiao Lin
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jintao Cheng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Linpei Zhang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, China
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Hueso-Gil A, Nyerges Á, Pál C, Calles B, de Lorenzo V. Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices. ACS Synth Biol 2020; 9:104-114. [PMID: 31794196 DOI: 10.1021/acssynbio.9b00375] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The features of the light-responsive cyanobacterial CcaSR regulatory module that determine interoperability of this optogenetic device between Escherichia coli and Pseudomonas putida have been examined. For this, all structural parts (i.e., ho1 and pcyA genes for synthesis of phycocyanobilin, the ccaS/ccaR system from Synechocystis, and its cognate downstream promoter) were maintained but their expression levels and stoichiometry diversified by (i) reassembling them together in a single broad host range, standardized vector and (ii) subjecting the noncoding regulatory sequences to multiple cycles of directed evolution with random genomic mutations (DIvERGE), a recombineering method that intensifies mutation rates within discrete DNA segments. Once passed to P. putida, various clones displayed a wide dynamic range, insignificant leakiness, and excellent capacity in response to green light. Inspection of the evolutionary intermediates pinpointed translational control as the main bottleneck for interoperability and suggested a general approach for easing the exchange of genetic cargoes between different species, i.e., optimization of relative expression levels and upturning of subcomplex stoichiometry.
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Affiliation(s)
- Angeles Hueso-Gil
- Systems Biology Program, Centro Nacional de Biotecnología, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged H-6726, Hungary
| | - Belén Calles
- Systems Biology Program, Centro Nacional de Biotecnología, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología, Campus de Cantoblanco, 28049 Madrid, Spain
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