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d'Oelsnitz S, Stofel SK, Love JD, Ellington AD. Snowprint: a predictive tool for genetic biosensor discovery. Commun Biol 2024; 7:163. [PMID: 38336860 PMCID: PMC10858194 DOI: 10.1038/s42003-024-05849-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Bioengineers increasingly rely on ligand-inducible transcription regulators for chemical-responsive control of gene expression, yet the number of regulators available is limited. Novel regulators can be mined from genomes, but an inadequate understanding of their DNA specificity complicates genetic design. Here we present Snowprint, a simple yet powerful bioinformatic tool for predicting regulator:operator interactions. Benchmarking results demonstrate that Snowprint predictions are significantly similar for >45% of experimentally validated regulator:operator pairs from organisms across nine phyla and for regulators that span five distinct structural families. We then use Snowprint to design promoters for 33 previously uncharacterized regulators sourced from diverse phylogenies, of which 28 are shown to influence gene expression and 24 produce a >20-fold dynamic range. A panel of the newly repurposed regulators are then screened for response to biomanufacturing-relevant compounds, yielding new sensors for a polyketide (olivetolic acid), terpene (geraniol), steroid (ursodiol), and alkaloid (tetrahydropapaverine) with induction ratios up to 10.7-fold. Snowprint represents a unique, protein-agnostic tool that greatly facilitates the discovery of ligand-inducible transcriptional regulators for bioengineering applications. A web-accessible version of Snowprint is available at https://snowprint.groov.bio .
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Affiliation(s)
- Simon d'Oelsnitz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Synthetic Biology HIVE, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Sarah K Stofel
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Joshua D Love
- Independent Web Developer, Bentonville, AR, 72712, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
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2
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Matteau D, Duval A, Baby V, Rodrigue S. Mesoplasma florum: a near-minimal model organism for systems and synthetic biology. Front Genet 2024; 15:1346707. [PMID: 38404664 PMCID: PMC10884336 DOI: 10.3389/fgene.2024.1346707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024] Open
Abstract
Mesoplasma florum is an emerging model organism for systems and synthetic biology due to its small genome (∼800 kb) and fast growth rate. While M. florum was isolated and first described almost 40 years ago, many important aspects of its biology have long remained uncharacterized due to technological limitations, the absence of dedicated molecular tools, and since this bacterial species has not been associated with any disease. However, the publication of the first M. florum genome in 2004 paved the way for a new era of research fueled by the rise of systems and synthetic biology. Some of the most important studies included the characterization and heterologous use of M. florum regulatory elements, the development of the first replicable plasmids, comparative genomics and transposon mutagenesis, whole-genome cloning in yeast, genome transplantation, in-depth characterization of the M. florum cell, as well as the development of a high-quality genome-scale metabolic model. The acquired data, knowledge, and tools will greatly facilitate future genome engineering efforts in M. florum, which could next be exploited to rationally design and create synthetic cells to advance fundamental knowledge or for specific applications.
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Affiliation(s)
- Dominick Matteau
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Anthony Duval
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Vincent Baby
- Centre de diagnostic vétérinaire de l'Université de Montréal, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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3
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Liu JQ, Min D, He RL, Cheng ZH, Wu J, Liu DF. Efficient and precise control of gene expression in Geobacter sulfurreducens through new genetic elements and tools for pollutant conversion. Biotechnol Bioeng 2023; 120:3001-3012. [PMID: 37209207 DOI: 10.1002/bit.28433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Geobacter species, exhibiting exceptional extracellular electron transfer aptitude, hold great potential for applications in pollution remediation, bioenergy production, and natural elemental cycles. Nonetheless, a scarcity of well-characterized genetic elements and gene expression tools constrains the effective and precise fine-tuning of gene expression in Geobacter species, thereby limiting their applications. Here, we examined a suite of genetic elements and developed a new genetic editing tool in Geobacter sulfurreducens to enhance their pollutant conversion capacity. First, the performances of the widely used inducible promoters, constitutive promoters, and ribosomal binding sites (RBSs) elements in G. sulfurreducens were quantitatively evaluated. Also, six native promoters with superior expression levels than constitutive promoters were identified on the genome of G. sulfurreducens. Employing the characterized genetic elements, the clustered regularly interspaced short palindromic repeats interference (CRISPRi) system was constructed in G. sulfurreducens to achieve the repression of an essential gene-aroK and morphogenic genes-ftsZ and mreB. Finally, applying the engineered strain to the reduction of tungsten trioxide (WO3 ), methyl orange (MO), and Cr(VI), We found that morphological elongation through ftsZ repression amplified the extracellular electron transfer proficiency of G. sulfurreducens and facilitated its contaminant transformation efficiency. These new systems provide rapid, versatile, and scalable tools poised to expedite advancements in Geobacter genomic engineering to favor environmental and other biotechnological applications.
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Affiliation(s)
- Jia-Qi Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Ru-Li He
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Zhou-Hua Cheng
- School of Life Sciences, University of Science & Technology of China, Hefei, China
| | - Jie Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
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Kretz J, Israel V, McIntosh M. Design-Build-Test of Synthetic Promoters for Inducible Gene Regulation in Alphaproteobacteria. ACS Synth Biol 2023; 12:2663-2675. [PMID: 37561940 DOI: 10.1021/acssynbio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Inducible gene expression is useful for biotechnological applications and for studying gene regulation and function in bacteria. Many inducible systems that perform in model organisms such as the Gammaproteobacterium Escherichia coli do not perform well in other bacteria that are of biotechnological interest. Typical problems include weak or leaky expression. Here, we describe an invention named ACIT (Alphaproteobacteria chromosomally integrating transcription-control cassette) that is carried on a suicide plasmid to enable insertion into the chromosome of the host. ACIT consists of multiple DNA fragments specifically arranged in a cassette that allows tight transcription control over any gene or gene cluster of interest following homologous recombination. At the heart of the invention is the ability to modify or exchange parts, e.g., promoters, to suit particular bacteria and growth conditions, allowing for customized gene expression control. Furthermore, ACIT provides a basis for a design-build-test approach for controlling gene expression in less studied bacteria. We describe examples of its control over pigment and exopolysaccharide production, growth, cell form, and social behavior in various Alphaproteobacteria.
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Affiliation(s)
- Jonas Kretz
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| | - Vera Israel
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
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Zhang Y, Xiao F, Zhang L, Ding Z, Shi G, Li Y. A New Mechanism of Carbon Metabolism and Acetic Acid Balance Regulated by CcpA. Microorganisms 2023; 11:2303. [PMID: 37764147 PMCID: PMC10535407 DOI: 10.3390/microorganisms11092303] [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: 08/17/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Catabolite control protein A (CcpA) is a critical regulator in Gram-positive bacteria that orchestrates carbon metabolism by coordinating the utilization of different carbon sources. Although it has been widely proved that CcpA helps prioritize the utilization of glucose over other carbon sources, this global regulator's precise mechanism of action remains unclear. In this study, a mutant Bacillus licheniformis deleted for CcpA was constructed. Cell growth, carbon utilization, metabolites and the transcription of key enzymes of the mutant strain were compared with that of the wild-type one. It was found that CcpA is involved in the regulation of glucose concentration metabolism in Bacillus. At the same time, CcpA regulates glucose metabolism by inhibiting acetic acid synthesis and pentose phosphate pathway key gene zwF. The conversion rate of acetic acid is increased by about 3.5 times after ccpA is deleted. The present study provides a new mechanism of carbon metabolism and acetic acid balance regulated by CcpA. On the one hand, this work deepens the understanding of the regulatory function of CcpA and provides a new view on the regulation of glucose metabolism. On the other hand, it is helpful to the transformation of B. licheniformis chassis microorganisms.
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Affiliation(s)
- Yupeng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Fengxu Xiao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.Z.); (F.X.); (L.Z.); (Z.D.); (G.S.)
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
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Hall AN, Hall BW, Kinney KJ, Olsen GG, Banta AB, Noguera DR, Donohue TJ, Peters JM. Tools for Genetic Engineering and Gene Expression Control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554875. [PMID: 37662258 PMCID: PMC10473679 DOI: 10.1101/2023.08.25.554875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts have the potential to form the backbone of the sustainable bioeconomy. Among the Alphaproteobacteria, Novosphingobium aromaticivorans, Rhodobacter sphaeroides, and Zymomonas mobilis, show particular promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for Z. mobilis, N. aromaticivorans and R. sphaeroides still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for N. aromaticivorans and R. sphaeroides to address these issues. We demonstrate that Tn7 transposition is an effective approach for introducing engineered DNA into the chromosome of N. aromaticivorans and R. sphaeroides. We screen a synthetic promoter library to identify inducible promoters with strong, regulated activity in both organisms. Combining Tn7 integration with promoters from our library, we establish CRISPR interference systems for N. aromaticivorans and R. sphaeroides that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these industrially important species and other Alphaproteobacteria.
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Affiliation(s)
- Ashley N. Hall
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin W. Hall
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kyle J. Kinney
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gabby G. Olsen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amy B. Banta
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Timothy J. Donohue
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Peters
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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7
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Pearson AN, Thompson MG, Kirkpatrick LD, Ho C, Vuu KM, Waldburger LM, Keasling JD, Shih PM. The pGinger Family of Expression Plasmids. Microbiol Spectr 2023; 11:e0037323. [PMID: 37212656 PMCID: PMC10269703 DOI: 10.1128/spectrum.00373-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023] Open
Abstract
The pGinger suite of expression plasmids comprises 43 plasmids that will enable precise constitutive and inducible gene expression in a wide range of Gram-negative bacterial species. Constitutive vectors are composed of 16 synthetic constitutive promoters upstream of red fluorescent protein (RFP), with a broad-host-range BBR1 origin and a kanamycin resistance marker. The family also has seven inducible systems (Jungle Express, Psal/NahR, Pm/XylS, Prha/RhaS, LacO1/LacI, LacUV5/LacI, and Ptet/TetR) controlling RFP expression on BBR1/kanamycin plasmid backbones. For four of these inducible systems (Jungle Express, Psal/NahR, LacO1/LacI, and Ptet/TetR), we created variants that utilize the RK2 origin and spectinomycin or gentamicin selection. Relevant RFP expression and growth data have been collected in the model bacterium Escherichia coli as well as Pseudomonas putida. All pGinger vectors are available via the Joint BioEnergy Institute (JBEI) Public Registry. IMPORTANCE Metabolic engineering and synthetic biology are predicated on the precise control of gene expression. As synthetic biology expands beyond model organisms, more tools will be required that function robustly in a wide range of bacterial hosts. The pGinger family of plasmids constitutes 43 plasmids that will enable both constitutive and inducible gene expression in a wide range of nonmodel Proteobacteria.
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Affiliation(s)
- Allison N. Pearson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Liam D. Kirkpatrick
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cindy Ho
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Khanh M. Vuu
- Joint BioEnergy Institute, Emeryville, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lucas M. Waldburger
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M. Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
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English MA, Alcantar MA, Collins JJ. A self‐propagating, barcoded transposon system for the dynamic rewiring of genomic networks. Mol Syst Biol 2023:e11398. [DOI: 10.15252/msb.202211398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
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Zhu Y, Gao H, Zhang J, Zhao J, Qi Q, Wang Q. De novo design of the global transcriptional factor Cra-regulated promoters enables highly sensitive glycolysis flux biosensor for dynamic metabolic control. Microb Biotechnol 2023; 16:605-617. [PMID: 36541030 PMCID: PMC9948231 DOI: 10.1111/1751-7915.14166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Glycolytic flux is a fundamental index in microbial cell factories. A glycolytic flux biosensor that can monitor glucose metabolism efficiency is a promising strategy in rewiring metabolic flux to balance growth and biosynthesis. A key design feature of the glycolytic flux biosensors is the interaction between the global transcriptional factor Cra and its regulated promoters. However, overexpression and mutation of Cra has unpredictable effects on global metabolism in Escherichia coli. Therefore, new orthogonal biosensor design strategies should be developed to circumvent metabolic issues. In this report, the promoters in glycolytic flux biosensor were replaced with synthetic promoters of varying strengths or phage-derived promoters, and the Cra DNA-binding sites were deployed into promoters at different positions and distances to yield biosensors. The de nova biosensors that depended on Cra could sense Fructose-1,6-diphosphate (FBP) with broad dynamic ranges and low basal leakage. Then the negative-response biosensors were applied to fine-tune the target ATP synthesis gene, leading to the desired increase in pyruvate production (the highest 9.66 g/L) and cell growth. Moreover, the membrane synthesis gene plsC was also dynamically activated by the positive-response biosensor, leading to effective accumulation of lycopene in the cell membrane and a 50-fold increase in lycopene titre (100.3 mg/L) when compared with the control strain, demonstrating the effective and broader usages of our biosensors.
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Affiliation(s)
- Yuan Zhu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaxiao Gao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Zhang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jingyu Zhao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Liu F, Zhou J, Hu M, Chen Y, Han J, Pan X, You J, Xu M, Yang T, Shao M, Zhang X, Rao Z. Efficient biosynthesis of (R)-mandelic acid from styrene oxide by an adaptive evolutionary Gluconobacter oxydans STA. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:8. [PMID: 36639820 PMCID: PMC9838050 DOI: 10.1186/s13068-023-02258-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/01/2023] [Indexed: 01/15/2023]
Abstract
BACKGROUND (R)-mandelic acid (R-MA) is a highly valuable hydroxyl acid in the pharmaceutical industry. However, biosynthesis of optically pure R-MA remains significant challenges, including the lack of suitable catalysts and high toxicity to host strains. Adaptive laboratory evolution (ALE) was a promising and powerful strategy to obtain specially evolved strains. RESULTS Herein, we report a new cell factory of the Gluconobacter oxydans to biocatalytic styrene oxide into R-MA by utilizing the G. oxydans endogenous efficiently incomplete oxidization and the epoxide hydrolase (SpEH) heterologous expressed in G. oxydans. With a new screened strong endogenous promoter P12780, the production of R-MA was improved to 10.26 g/L compared to 7.36 g/L of using Plac. As R-MA showed great inhibition for the reaction and toxicity to cell growth, adaptive laboratory evolution (ALE) strategy was introduced to improve the cellular R-MA tolerance. The adapted strain that can tolerate 6 g/L R-MA was isolated (named G. oxydans STA), while the wild-type strain cannot grow under this stress. The conversion rate was increased from 0.366 g/L/h of wild type to 0.703 g/L/h by the recombinant STA, and the final R-MA titer reached 14.06 g/L. Whole-genome sequencing revealed multiple gene-mutations in STA, in combination with transcriptome analysis under R-MA stress condition, we identified five critical genes that were associated with R-MA tolerance, among which AcrA overexpression could further improve R-MA titer to 15.70 g/L, the highest titer reported from bulk styrene oxide substrate. CONCLUSIONS The microbial engineering with systematic combination of static regulation, ALE, and transcriptome analysis strategy provides valuable solutions for high-efficient chemical biosynthesis, and our evolved G. oxydans would be better to serve as a chassis cell for hydroxyl acid production.
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Affiliation(s)
- Fei Liu
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Junping Zhou
- grid.469325.f0000 0004 1761 325XSchool of Biotechnology, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Mengkai Hu
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Yan Chen
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Jin Han
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xuewei Pan
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Jiajia You
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Meijuan Xu
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Taowei Yang
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Minglong Shao
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xian Zhang
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Zhiming Rao
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
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11
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Spanka DT, Grützner J, Jäger A, Klug G. A Small RNA, UdsC, Interacts with the R poHII mRNA and Affects the Motility and Stress Resistance of Rhodobacter sphaeroides. Int J Mol Sci 2022; 23:ijms232415486. [PMID: 36555125 PMCID: PMC9779115 DOI: 10.3390/ijms232415486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
sRNAs have an important role in the regulation of bacterial gene expression. The sRNA, UdsC, of Rhodobacter sphaeroides is derived from the 3' UTR of the RSP_7527 mRNA, which encodes a hypothetical protein. Here, we showed the effect of UdsC on the resistance of Rhodobacter sphaeroides to hydrogen peroxide and on its motility. In vitro binding assays supported the direct interaction of UdsC with the 5' UTR of the rpoHII mRNA. RpoHII is an alternative sigma factor with an important role in stress responses in R. sphaeroides, including its response to hydrogen peroxide. We also demonstrated that RpoHII controls the expression of the torF gene, which encodes an important regulator of motility genes. This strongly suggested that the observed effect of UdsC on TorF expression is indirect and mediated by RpoHII.
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12
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Leonard AC, Whitehead TA. Design and engineering of genetically encoded protein biosensors for small molecules. Curr Opin Biotechnol 2022; 78:102787. [PMID: 36058141 DOI: 10.1016/j.copbio.2022.102787] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 12/14/2022]
Abstract
Genetically encoded protein biosensors controlled by small organic molecules are valuable tools for many biotechnology applications, including control of cellular decisions in living cells. Here, we review recent advances in protein biosensor design and engineering for binding to novel ligands. We categorize sensor architecture as either integrated or portable, where portable biosensors uncouple molecular recognition from signal transduction. Proposed advances to improve portable biosensor development include standardizing a limited set of protein scaffolds, and automating ligand-compatibility screening and ligand-protein-interface design.
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Affiliation(s)
- Alison C Leonard
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA.
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13
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Otoupal PB, Cress BF, Doudna JA, Schoeniger J. CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors. Nucleic Acids Res 2022; 50:8986-8998. [PMID: 35950485 PMCID: PMC9410913 DOI: 10.1093/nar/gkac680] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/19/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022] Open
Abstract
Tools for synthetically controlling gene expression are a cornerstone of genetic engineering. CRISPRi and CRISPRa technologies have been applied extensively for programmable modulation of gene transcription, but there are few such tools for targeted modulation of protein translation rates. Here, we employ CRISPR-Cas13 as a programmable activator of translation. We develop a novel variant of the catalytically-deactivated Cas13d enzyme dCasRx by fusing it to translation initiation factor IF3. We demonstrate dCasRx-IF3's ability to enhance expression 21.3-fold above dCasRx when both are targeted to the start of the 5' untranslated region of mRNA encoding red fluorescent protein in Escherichia coli. Activation of translation is location-dependent, and we show dCasRx-IF3 represses translation when targeted to the ribosomal binding site, rather than enhancing it. We provide evidence that dCasRx-IF3 targeting enhances mRNA stability relative to dCasRx, providing mechanistic insights into how this new tool functions to enhance gene expression. We also demonstrate targeted upregulation of native LacZ 2.6-fold, showing dCasRx-IF3's ability to enhance expression of endogenous genes. dCasRx-IF3 requires no additional host modification to influence gene expression. This work outlines a novel approach, CRISPR-RNAa, for post-transcriptional control of translation to activate gene expression.
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Affiliation(s)
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA,California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA,Department of Chemistry, University of California, Berkeley, CA, USA,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA,Gladstone Institutes, University of California, San Francisco, CA, USA
| | - Joseph S Schoeniger
- To whom correspondence should be addressed. Tel: +1 925 294 2955; Fax: +1 925 294 3020;
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14
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Nasr M, Timmins LR, Martin VJJ, Kwan DH. A Versatile Transcription Factor Biosensor System Responsive to Multiple Aromatic and Indole Inducers. ACS Synth Biol 2022; 11:1692-1698. [PMID: 35316041 PMCID: PMC9017570 DOI: 10.1021/acssynbio.2c00063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Indexed: 12/26/2022]
Abstract
Allosteric transcription factor (aTF) biosensors are valuable tools for engineering microbes toward a multitude of applications in metabolic engineering, biotechnology, and synthetic biology. One of the challenges toward constructing functional and diverse biosensors in engineered microbes is the limited toolbox of identified and characterized aTFs. To overcome this, extensive bioprospecting of aTFs from sequencing databases, as well as aTF ligand-specificity engineering are essential in order to realize their full potential as biosensors for novel applications. In this work, using the TetR-family repressor CmeR from Campylobacter jejuni, we construct aTF genetic circuits that function as salicylate biosensors in the model organisms Escherichia coli and Saccharomyces cerevisiae. In addition to salicylate, we demonstrate the responsiveness of CmeR-regulated promoters to multiple aromatic and indole inducers. This relaxed ligand specificity of CmeR makes it a useful tool for detecting molecules in many metabolic engineering applications, as well as a good target for directed evolution to engineer proteins that are able to detect new and diverse chemistries.
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Affiliation(s)
- Mohamed
A. Nasr
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
| | - Logan R. Timmins
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
| | - Vincent J. J. Martin
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
| | - David H. Kwan
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
- Department
of Chemistry and Biochemistry, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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15
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Cellular Computational Logic Using Toehold Switches. Int J Mol Sci 2022; 23:ijms23084265. [PMID: 35457085 PMCID: PMC9033136 DOI: 10.3390/ijms23084265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/16/2022] Open
Abstract
The development of computational logic that carries programmable and predictable features is one of the key requirements for next-generation synthetic biological devices. Despite considerable progress, the construction of synthetic biological arithmetic logic units presents numerous challenges. In this paper, utilizing the unique advantages of RNA molecules in building complex logic circuits in the cellular environment, we demonstrate the RNA-only bitwise logical operation of XOR gates and basic arithmetic operations, including a half adder, a half subtractor, and a Feynman gate, in Escherichia coli. Specifically, de-novo-designed riboregulators, known as toehold switches, were concatenated to enhance the functionality of an OR gate, and a previously utilized antisense RNA strategy was further optimized to construct orthogonal NIMPLY gates. These optimized synthetic logic gates were able to be seamlessly integrated to achieve final arithmetic operations on small molecule inputs in cells. Toehold-switch-based ribocomputing devices may provide a fundamental basis for synthetic RNA-based arithmetic logic units or higher-order systems in cells.
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16
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d’Oelsnitz S, Nguyen V, Alper HS, Ellington AD. Evolving a Generalist Biosensor for Bicyclic Monoterpenes. ACS Synth Biol 2022; 11:265-272. [PMID: 34985281 DOI: 10.1021/acssynbio.1c00402] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prokaryotic transcription factors can be repurposed as analytical and synthetic tools for precise chemical measurement and regulation. Monoterpenes encompass a broad chemical family that are commercially valuable as flavors, cosmetics, and fragrances, but have proven difficult to measure, especially in cells. Herein, we develop genetically encoded, generalist monoterpene biosensors by using directed evolution to expand the effector specificity of the camphor-responsive TetR-family regulator CamR from Pseudomonas putida. Using a novel negative selection coupled with a high-throughput positive screen (Seamless Enrichment of Ligand-Inducible Sensors, SELIS), we evolve CamR biosensors that can recognize four distinct monoterpenes: borneol, fenchol, eucalyptol, and camphene. Different evolutionary trajectories surprisingly yielded common mutations, emphasizing the utility of CamR as a platform for creating generalist biosensors. Systematic promoter optimization driving the reporter increased the system's signal-to-noise ratio to 150-fold. These sensors can serve as a starting point for the high-throughput screening and dynamic regulation of bicyclic monoterpene production strains.
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Affiliation(s)
- Simon d’Oelsnitz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Vylan Nguyen
- Freshman Research Initiative, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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17
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Singh RP, Shadan A, Ma Y. Biotechnological Applications of Probiotics: A Multifarious Weapon to Disease and Metabolic Abnormality. Probiotics Antimicrob Proteins 2022; 14:1184-1210. [PMID: 36121610 PMCID: PMC9483357 DOI: 10.1007/s12602-022-09992-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Consumption of live microorganisms "Probiotics" for health benefits and well-being is increasing worldwide. Their use as a therapeutic approach to confer health benefits has fascinated humans for centuries; however, its conceptuality gradually evolved with methodological advancement, thereby improving our understanding of probiotics-host interaction. However, the emerging concern regarding safety aspects of live microbial is enhancing the interest in non-viable or microbial cell extracts, as they could reduce the risks of microbial translocation and infection. Due to technical limitations in the production and formulation of traditionally used probiotics, the scientific community has been focusing on discovering new microbes to be used as probiotics. In many scientific studies, probiotics have been shown as potential tools to treat metabolic disorders such as obesity, type-2 diabetes, non-alcoholic fatty liver disease, digestive disorders (e.g., acute and antibiotic-associated diarrhea), and allergic disorders (e.g., eczema) in infants. However, the mechanistic insight of strain-specific probiotic action is still unknown. In the present review, we analyzed the scientific state-of-the-art regarding the mechanisms of probiotic action, its physiological and immuno-modulation on the host, and new direction regarding the development of next-generation probiotics. We discuss the use of recently discovered genetic tools and their applications for engineering the probiotic bacteria for various applications including food, biomedical applications, and other health benefits. Finally, the review addresses the future development of biological techniques in combination with clinical and preclinical studies to explain the molecular mechanism of action, and discover an ideal multifunctional probiotic bacterium.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand India
| | - Afreen Shadan
- Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand India
| | - Ying Ma
- College of Resource and Environment, Southwest University, Chongqing, China
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18
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Keasling J, Garcia Martin H, Lee TS, Mukhopadhyay A, Singer SW, Sundstrom E. Microbial production of advanced biofuels. Nat Rev Microbiol 2021; 19:701-715. [PMID: 34172951 DOI: 10.1038/s41579-021-00577-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Concerns over climate change have necessitated a rethinking of our transportation infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced by engineered microorganisms that use a renewable carbon source. Two biofuels, ethanol and biodiesel, have made inroads in displacing petroleum-based fuels, but their uptake has been limited by the amounts that can be used in conventional engines and by their cost. Advanced biofuels that mimic petroleum-based fuels are not limited by the amounts that can be used in existing transportation infrastructure but have had limited uptake due to costs. In this Review, we discuss engineering metabolic pathways to produce advanced biofuels, challenges with substrate and product toxicity with regard to host microorganisms and methods to engineer tolerance, and the use of functional genomics and machine learning approaches to produce advanced biofuels and prospects for reducing their costs.
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Affiliation(s)
- Jay Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA. .,Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Center for Biosustainability, Danish Technical University, Lyngby, Denmark. .,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,DOE Agile BioFoundry, Emeryville, CA, USA.,BCAM,Basque Center for Applied Mathematics, Bilbao, Spain.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eric Sundstrom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, USA
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19
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Chen JX, Lim B, Steel H, Song Y, Ji M, Huang WE. Redesign of ultrasensitive and robust RecA gene circuit to sense DNA damage. Microb Biotechnol 2021; 14:2481-2496. [PMID: 33661573 PMCID: PMC8601168 DOI: 10.1111/1751-7915.13767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 01/10/2023] Open
Abstract
SOS box of the recA promoter, PVRecA from Vibrio natriegens was characterized, cloned and expressed in a probiotic strain E. coli Nissle 1917. This promoter was then rationally engineered according to predicted interactions between LexA repressor and PVRecA . The redesigned PVRecA-AT promoter showed a sensitive and robust response to DNA damage induced by UV and genotoxic compounds. Rational design of PVRecA coupled to an amplification gene circuit increased circuit output amplitude 4.3-fold in response to a DNA damaging compound mitomycin C. A TetR-based negative feedback loop was added to the PVRecA-AT amplifier to achieve a robust SOS system, resistant to environmental fluctuations in parameters including pH, temperature, oxygen and nutrient conditions. We found that E. coli Nissle 1917 with optimized PVRecA-AT adapted to UV exposure and increased SOS response 128-fold over 40 h cultivation in turbidostat mini-reactor. We also showed the potential of this PVRecA-AT system as an optogenetic actuator, which can be controlled spatially through UV radiation. We demonstrated that the optimized SOS responding gene circuits were able to detect carcinogenic biomarker molecules with clinically relevant concentrations. The ultrasensitive SOS gene circuits in probiotic E. coli Nissle 1917 would be potentially useful for bacterial diagnosis.
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Affiliation(s)
- Jack X. Chen
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Boon Lim
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Harrison Steel
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Yizhi Song
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Mengmeng Ji
- Oxford Suzhou Centre for Advanced ResearchSuzhou215123China
| | - Wei E. Huang
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
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20
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Holgado A, Braun H, Verstraete K, Vanneste D, Callewaert N, Savvides SN, Afonina IS, Beyaert R. Single-Chain Soluble Receptor Fusion Proteins as Versatile Cytokine Inhibitors. Front Immunol 2020; 11:1422. [PMID: 32754154 PMCID: PMC7370943 DOI: 10.3389/fimmu.2020.01422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/02/2020] [Indexed: 01/08/2023] Open
Abstract
Cytokines are small secreted proteins that among many functions also play key roles in the orchestration of inflammation in host defense and disease. Over the past years, a large number of biologics have been developed to target cytokines in disease, amongst which soluble receptor fusion proteins have shown some promise in pre-clinical studies. We have previously shown proof-of-concept for the therapeutic targeting of interleukin (IL)-33 in airway inflammation using a newly developed biologic, termed IL-33trap, comprising the ectodomains of the cognate receptor ST2 and the co-receptor IL-1RAcP fused into a single-chain recombinant fusion protein. Here we extend the biophysical and biological characterization of IL-33trap variants, and show that IL-33trap is a stable protein with a monomeric profile both at physiological temperatures and during liquid storage at 4°C. Reducing the N-glycan heterogeneity and complexity of IL-33trap via GlycoDelete engineering neither affects its stability nor its inhibitory activity against IL-33. We also report that IL-33trap specifically targets biologically active IL-33 splice variants. Finally, we document the generation and antagonistic activity of a single-chain IL-4/13trap, which inhibits both IL-4 and IL-13 signaling. Collectively, these results illustrate that single-chain soluble receptor fusion proteins against IL-4, IL-13, and IL-33 are novel biologics that might not only be of interest for research purposes and further interrogation of the role of their target cytokines in physiology and disease, but may also complement monoclonal antibodies for the treatment of allergic and other inflammatory diseases.
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Affiliation(s)
- Aurora Holgado
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Harald Braun
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kenneth Verstraete
- Center for Inflammation Research, Unit for Structural Biology, VIB, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Domien Vanneste
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Nico Callewaert
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Savvas N Savvides
- Center for Inflammation Research, Unit for Structural Biology, VIB, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Inna S Afonina
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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21
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Behle A, Saake P, Germann AT, Dienst D, Axmann IM. Comparative Dose-Response Analysis of Inducible Promoters in Cyanobacteria. ACS Synth Biol 2020; 9:843-855. [PMID: 32134640 DOI: 10.1021/acssynbio.9b00505] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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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22
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Fan C, Davison PA, Habgood R, Zeng H, Decker CM, Gesell Salazar M, Lueangwattanapong K, Townley HE, Yang A, Thompson IP, Ye H, Cui Z, Schmidt F, Hunter CN, Huang WE. Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology. Proc Natl Acad Sci U S A 2020; 117:6752-6761. [PMID: 32144140 PMCID: PMC7104398 DOI: 10.1073/pnas.1918859117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A type of chromosome-free cell called SimCells (simple cells) has been generated from Escherichia coli, Pseudomonas putida, and Ralstonia eutropha. The removal of the native chromosomes of these bacteria was achieved by double-stranded breaks made by heterologous I-CeuI endonuclease and the degradation activity of endogenous nucleases. We have shown that the cellular machinery remained functional in these chromosome-free SimCells and was able to process various genetic circuits. This includes the glycolysis pathway (composed of 10 genes) and inducible genetic circuits. It was found that the glycolysis pathway significantly extended longevity of SimCells due to its ability to regenerate ATP and NADH/NADPH. The SimCells were able to continuously express synthetic genetic circuits for 10 d after chromosome removal. As a proof of principle, we demonstrated that SimCells can be used as a safe agent (as they cannot replicate) for bacterial therapy. SimCells were used to synthesize catechol (a potent anticancer drug) from salicylic acid to inhibit lung, brain, and soft-tissue cancer cells. SimCells represent a simplified synthetic biology chassis that can be programmed to manufacture and deliver products safely without interference from the host genome.
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Affiliation(s)
- Catherine Fan
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Robert Habgood
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom
| | - Hong Zeng
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom
| | - Christoph M Decker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | | | - Helen E Townley
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom
| | - Hua Ye
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom
| | - Zhanfeng Cui
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- Proteomics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, United Kingdom;
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23
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Calles B, Goñi‐Moreno Á, de Lorenzo V. Digitalizing heterologous gene expression in Gram-negative bacteria with a portable ON/OFF module. Mol Syst Biol 2019; 15:e8777. [PMID: 31885200 PMCID: PMC6920698 DOI: 10.15252/msb.20188777] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 01/24/2023] Open
Abstract
While prokaryotic promoters controlled by signal-responding regulators typically display a range of input/output ratios when exposed to cognate inducers, virtually no naturally occurring cases are known to have an OFF state of zero transcription-as ideally needed for synthetic circuits. To overcome this problem, we have modelled and implemented a simple digitalizer module that completely suppresses the basal level of otherwise strong promoters in such a way that expression in the absence of induction is entirely impeded. The circuit involves the interplay of a translation-inhibitory sRNA with the translational coupling of the gene of interest to a repressor such as LacI. The digitalizer module was validated with the strong inducible promoters Pm (induced by XylS in the presence of benzoate) and PalkB (induced by AlkS/dicyclopropyl ketone) and shown to perform effectively in both Escherichia coli and the soil bacterium Pseudomonas putida. The distinct expression architecture allowed cloning and conditional expression of, e.g. colicin E3, one molecule of which per cell suffices to kill the host bacterium. Revertants that escaped ColE3 killing were not found in hosts devoid of insertion sequences, suggesting that mobile elements are a major source of circuit inactivation in vivo.
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Affiliation(s)
- Belén Calles
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSICMadridSpain
| | - Ángel Goñi‐Moreno
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSICMadridSpain
- Present address:
School of ComputingNewcastle UniversityNewcastle upon TyneUK
| | - Víctor de Lorenzo
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSICMadridSpain
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Sharshar MM, Samak NA, Hao X, Mu T, Zhong W, Yang M, Peh S, Ambreen S, Xing J. Enhanced growth-driven stepwise inducible expression system development in haloalkaliphilic desulfurizing Thioalkalivibrio versutus. BIORESOURCE TECHNOLOGY 2019; 288:121486. [PMID: 31128536 DOI: 10.1016/j.biortech.2019.121486] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 05/13/2023]
Abstract
Highly toxic and flammable H2S gas has become an environmental threat. Because of its ability to efficiently remove H2S by oxidation, Thioalkalivibrio versutus is gaining more attention. Haloalkaliphilic autotrophs, like the bio-desulfurizing T. versutus, grow weakly. Weak growth makes any trial for developing potent genetic tools required for genetic engineering far from achieved. In this study, the fed-batch strategy improved T. versutus growth by 1.6 fold in maximal growth rate, 9-fold in O.D600 values and about 3-fold in biomass and protein productions. The strategy also increased the favorable desulfurization product, sulfur, by 2.7 fold in percent yield and 1.5-fold in diameter. A tight iron-inducible expression system for T. versutus was successfully developed. The system was derived from fed-batch cultivation coupled with new design, build, test and validate (DPTV) approach. The inducible system was validated by toxin expression. Fed-batch cultivation coupled with DPTV approach could be applied to other autotrophs.
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Affiliation(s)
- Moustafa Mohamed Sharshar
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nadia Abdrabo Samak
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Processes Design and Development Department, Egyptian Petroleum Research Institute, Nasr City, 11727 Cairo, Egypt
| | - Xuemi Hao
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingzhen Mu
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Wei Zhong
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maohua Yang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Sumit Peh
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sadaf Ambreen
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Genomics and Precision Medicine, Institute of Genomics, CAS, Beijing 100101, China
| | - Jianmin Xing
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences (CAS), Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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