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Serebrinsky-Duek K, Barra M, Danino T, Garrido D. Engineered Bacteria for Short-Chain-Fatty-Acid-Repressed Expression of Biotherapeutic Molecules. Microbiol Spectr 2023; 11:e0004923. [PMID: 36939337 PMCID: PMC10101121 DOI: 10.1128/spectrum.00049-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/20/2023] [Indexed: 03/21/2023] Open
Abstract
Short-chain fatty acids (SCFA) such as propionate and butyrate are critical metabolites produced by the gut microbiota. Microbiome dysbiosis resulting in altered SCFA profiles is associated with certain diseases, including inflammatory bowel diseases (IBD), characterized by a reduction in butyrate concentration and active intestinal inflammation. There is an increasing interest in the use of engineered bacteria as diagnostic and therapeutic tools for gut diseases. In this study, we developed genetic circuits capable of sensing SCFA concentrations to build biosensors that express a response protein (superfolder green fluorescent protein [sfGFP]) in amounts inversely proportional to the SCFA concentration. We also built biotherapeutics expressing the cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) using the same logic. The propionate biotherapeutic expressed larger amounts of mouse GM-CSF in the absence of propionate. The butyrate biotherapeutics presented the expected behavior only at the beginning of the kinetics and an accelerated response in the absence of butyrate. Overall, these genetic systems may function as complementary diagnostic tools for measuring SCFAs and as delivery vehicles for biotherapeutic molecules. IMPORTANCE Short-chain fatty acids are key molecules produced by the gut microbiome. Their concentrations are altered in certain diseases. Here, we created molecular biosensors that quantify the absence of propionate and butyrate, using logic "NOT" gates and bacterial promoters. Finally, we show that these genetic systems could be useful for the delivery of therapeutic molecules in the gut, in the absence of these acids.
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Affiliation(s)
- Kineret Serebrinsky-Duek
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maria Barra
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, New York, USA
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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Gongerowska-Jac M, Szafran MJ, Jakimowicz D. Combining transposon mutagenesis and reporter genes to identify novel regulators of the topA promoter in Streptomyces. Microb Cell Fact 2021; 20:99. [PMID: 33985526 PMCID: PMC8120823 DOI: 10.1186/s12934-021-01590-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying the regulatory factors that control transcriptional activity is a major challenge of gene expression studies. Here, we describe the application of a novel approach for in vivo identification of regulatory proteins that may directly or indirectly control the transcription of a promoter of interest in Streptomyces. RESULTS A method based on the combination of Tn5 minitransposon-driven random mutagenesis and lux reporter genes was applied for the first time for the Streptomyces genus. As a proof of concept, we studied the topA supercoiling-sensitive promoter, whose activity is dependent on unknown regulatory factors. We found that the sco4804 gene product positively influences topA transcription in S. coelicolor, demonstrating SCO4804 as a novel player in the control of chromosome topology in these bacteria. CONCLUSIONS Our approach allows the identification of novel Streptomyces regulators that may be critical for the regulation of gene expression in these antibiotic-producing bacteria.
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Yang Z, Sun Q, Tan G, Zhang Q, Wang Z, Li C, Qi F, Wang W, Zhang L, Li Z. Engineering thermophilic Geobacillus thermoglucosidasius for riboflavin production. Microb Biotechnol 2020; 14:363-373. [PMID: 32096925 PMCID: PMC7936320 DOI: 10.1111/1751-7915.13543] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 01/17/2023] Open
Abstract
The potential advantages for fermentation production of chemicals at high temperatures are attractive, such as promoting the rate of biochemical reactions, reducing the risk of contamination and the energy consumption for fermenter cooling. In this work, we de novo engineered the thermophile Geobacillus thermoglucosidasius to produce riboflavin, since this bacterium can ferment diverse carbohydrates at an optimal temperature of 60°C with a high growth rate. We first introduced a heterogeneous riboflavin biosynthetic gene cluster and enabled the strain to produce detectable riboflavin (28.7 mg l−1). Then, with the aid of an improved gene replacement method, we preformed metabolic engineering in this strain, including replacement of ribCGtg with a mutant allele to weaken the consumption of riboflavin, manipulation of purine pathway to enhance precursor supply, deletion of ccpNGtg to tune central carbon catabolism towards riboflavin production and elimination of the lactate dehydrogenase gene to block the dominating product lactic acid. Finally, the engineered strain could produce riboflavin with the titre of 1034.5 mg l−1 after 12‐h fermentation in a mineral salt medium, indicating G. thermoglucosidasius is a promising host to develop high‐temperature cell factory of riboflavin production. This is the first demonstration of riboflavin production in thermophilic bacteria at an elevated temperature.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Xuhui District, Shanghai, 200237, China
| | - Qingqing Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Gaoyi Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Xuhui District, Shanghai, 200237, China
| | - Quanwei Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Zhengduo Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Xuhui District, Shanghai, 200237, China
| | - Chuan Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Xuhui District, Shanghai, 200237, China
| | - Fengxian Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Weishan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Xuhui District, Shanghai, 200237, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Xuhui District, Shanghai, 200237, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
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Zhu J, Chen Z, Li J, Wen Y. AvaR1, a Butenolide-Type Autoregulator Receptor in Streptomyces avermitilis, Directly Represses Avenolide and Avermectin Biosynthesis and Multiple Physiological Responses. Front Microbiol 2017; 8:2577. [PMID: 29312254 PMCID: PMC5744401 DOI: 10.3389/fmicb.2017.02577] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/11/2017] [Indexed: 11/13/2022] Open
Abstract
Avermectins are commercially important anthelmintic antibiotics produced by Streptomyces avermitilis. The homologous TetR-family transcriptional regulators AvaR1 and AvaR2 in this species were identified previously as receptors of avenolide, a novel butenolide-type autoregulator signal required for triggering avermectin biosynthesis. AvaR2 was found to be an important pleiotropic regulator in repression of avermectin and avenolide production and cell growth, whereas the regulatory role of AvaR1 remains unclear. Investigation of AvaR1 function in the present study showed that it had no effect on cell growth or morphological differentiation, but inhibited avenolide and avermectin production mainly through direct repression of aco (the key enzyme gene for avenolide biosynthesis) and aveR (the cluster-situated activator gene). AvaR1 also directly repressed its own gene (avaR1) and two adjacent homologous genes (avaR2 and avaR3). Binding sites of AvaR1 on these five target promoter regions completely overlapped those of AvaR2, leading to the same consensus binding motif. However, AvaR1 and AvaR2 had both common and exclusive target genes, indicating that they cross-regulate diverse physiological processes. Ten novel identified AvaR1 targets are involved in primary metabolism, stress responses, ribosomal protein synthesis, and cyclic nucleotide degration, reflecting a pleiotropic role of AvaR1. Competitive EMSAs and GST pull-down assays showed that AvaR1 and AvaR2 competed for the same binding regions, and could form a heterodimer and homodimers, suggesting that AvaR1 and AvaR2 compete and cooperate to regulate their common target genes. These findings provide a more comprehensive picture of the cellular responses mediated by AvaR1 and AvaR2 regulatory networks in S. avermitilis.
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Affiliation(s)
- Jianya Zhu
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Fishery Biotechnology, Beijing Fisheries Research Institute, Beijing, China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jilun Li
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ying Wen
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
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Significance of Heavy-Ion Beam Irradiation-Induced Avermectin B1a Production by Engineered Streptomyces avermitilis. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5373262. [PMID: 28243599 PMCID: PMC5294878 DOI: 10.1155/2017/5373262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/09/2016] [Accepted: 10/23/2016] [Indexed: 12/21/2022]
Abstract
Heavy-ion irradiation technology has advantages over traditional methods of mutagenesis. Heavy-ion irradiation improves the mutation rate, broadens the mutation spectrum, and shortens the breeding cycle. However, few data are currently available regarding its effect on Streptomyces avermitilis morphology and productivity. In this study, the influence of heavy-ion irradiation on S. avermitilis when cultivated in approximately 10 L stirred-tank bioreactors was investigated. The specific productivity of the avermectin (AVM) B1a-producing mutant S. avermitilis 147-G58 increased notably, from 3885 to 5446 μg/mL, approximately 1.6-fold, compared to the original strain. The mycelial morphology of the mutant fermentation processes was microscopically examined. Additionally, protein and metabolite identification was performed by using SDS-PAGE, 2- and 3-dimensional electrophoresis (2DE and 3DE). The results showed that negative regulation gene deletion of mutants led to metabolic process upregulating expression of protein and improving the productivity of an avermectin B1a. The results showed that the heavy-ion beam irradiation dose that corresponded to optimal production was well over the standard dose, at approximately 80 Gy at 220 AMeV (depending on the strain). This study provides reliable data and a feasible method for increasing AVM productivity in industrial processes.
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Zhu J, Sun D, Liu W, Chen Z, Li J, Wen Y. AvaR2, a pseudo γ-butyrolactone receptor homologue from Streptomyces avermitilis, is a pleiotropic repressor of avermectin and avenolide biosynthesis and cell growth. Mol Microbiol 2016; 102:562-578. [PMID: 27502190 DOI: 10.1111/mmi.13479] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2016] [Indexed: 11/27/2022]
Abstract
Avermectins produced by Streptomyces avermitilis are effective anthelmintic agents. The autoregulatory signalling molecule that triggers avermectin biosynthesis is a novel butenolide-type molecule, avenolide, rather than common γ-butyrolactones (GBLs). We identified AvaR2, a pseudo GBL receptor homologue, as an important repressor of avermectin and avenolide biosynthesis and cell growth. AvaR2 directly repressed transcription of aveR (the ave cluster-situated activator gene), aco (a key gene for avenolide biosynthesis), its own gene (avaR2) and two other GBL receptor homologous genes (avaR1 and avaR3) by binding to their promoter regions. The aveR promoter had the highest affinity for AvaR2. A consensus 18 bp ARE (autoregulatory element)-like sequence was found in the AvaR2-binding regions of these five target genes. Eleven novel AvaR2 targets were identified, including genes involved in primary metabolism, ribosomal protein synthesis, and stress responses. AvaR2 bound and responded to endogenous avenolide and exogenous antibiotics jadomycin B (JadB) and aminoglycosides to modulate its DNA-binding activity. Our findings help to clarify the roles of pseudo GBL receptors as pleiotropic regulators and as receptors for new type autoregulator and exogenous antibiotic signal. A pseudo GBL receptor-mediated antibiotic signalling transduction system may be a common strategy that facilitates Streptomyces interspecies communication and survival in complex environments.
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Affiliation(s)
- Jianya Zhu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Di Sun
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wenshuai Liu
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhi Chen
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jilun Li
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ying Wen
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Wang W, Yang T, Li Y, Li S, Yin S, Styles K, Corre C, Yang K. Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts. ACS Synth Biol 2016; 5:765-73. [PMID: 27100123 DOI: 10.1021/acssynbio.6b00087] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Precise control of gene expression using exogenous factors is of great significance. To develop ideal inducible expression systems for streptomycetes, new genetic parts, oxytetracycline responsive repressor OtrR, operator otrO, and promoter otrBp from Streptomyces rimosus, were selected de novo and characterized in vivo and in vitro. OtrR showed strong affinity to otrO (KD = 1.7 × 10(-10) M) and oxytetracycline induced dissociation of the OtrR/DNA complex in a concentration-dependent manner. On the basis of these genetic parts, a synthetic inducible expression system Potr* was optimized. Induction of Potr* with 0.01-4 μM of oxytetracycline triggered a wide-range expression level of gfp reporter gene in different Streptomyces species. Benchmarking Potr* against the widely used constitutive promoters ermE* and kasOp* revealed greatly enhanced levels of expression when Potr* was fully induced. Finally, Potr* was used as a tool to activate and optimize the expression of the silent jadomycin biosynthetic gene cluster in Streptomyces venezuelae. Altogether, the synthetic Potr* presents a new versatile tool for fine-tuning gene expression in streptomycetes.
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Affiliation(s)
- Weishan Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| | - Tongjian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, People’s Republic of China
| | - Yihong Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| | - Shanshan Li
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| | - Shouliang Yin
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
| | - Kathryn Styles
- School
of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christophe Corre
- School
of Life Sciences and Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Keqian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 West Beichen Road, Chaoyang District, Beijing 100101, People’s Republic of China
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