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Huang X, Tang Q, Liu S, Li C, Li Y, Sun Y, Ding X, Xia L, Hu S. Discovery of an antitumor compound from xenorhabdus stockiae HN_xs01. World J Microbiol Biotechnol 2024; 40:101. [PMID: 38366186 DOI: 10.1007/s11274-024-03915-1] [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: 04/25/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Xenorhabdus, known for its symbiotic relationship with Entomopathogenic nematodes (EPNs), belongs to the Enterobacteriaceae family. This dual-host symbiotic nematode exhibits pathogenic traits, rendering it a promising biocontrol agent against insects. Our prior investigations revealed that Xenorhabdus stockiae HN_xs01, isolated in our laboratory, demonstrates exceptional potential in halting bacterial growth and displaying anti-tumor activity. Subsequently, we separated and purified the supernatant of the HN_xs01 strain and obtained a new compound with significant inhibitory activity on tumor cells, which we named XNAE. Through LC-MS analysis, the mass-to-nucleus ratio of XNAE was determined to be 254.24. Our findings indicated that XNAE exerts a time- and dose-dependent inhibition on B16 and HeLa cells. After 24 h, its IC50 for B16 and HeLa cells was 30.178 µg/mL and 33.015 µg/mL, respectively. Electron microscopy revealed conspicuous damage to subcellular structures, notably mitochondria and the cytoskeleton, resulting in a notable reduction in cell numbers among treated tumor cells. Interestingly, while XNAE exerted a more pronounced inhibitory effect on B16 cells compared to HeLa cells, it showed no discernible impact on HUVEC cells. Treatment of B16 cells with XNAE induced early apoptosis and led to cell cycle arrest in the G2 phase, as evidenced by flow cytometry analysis. The impressive capability of X. stockiae HN_xs01 in synthesizing bioactive secondary metabolites promises to significantly expand the reservoir of natural products. Further exploration to identify the bioactivity of these compounds holds the potential to shed light on their roles in bacteria-host interaction. Overall, these outcomes underscore the promising potential of XNAE as a bioactive compound for tumor treatment.
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Affiliation(s)
- Xiyin Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Qiong Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Siqin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Chen Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Yaoguang Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Yunjun Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China.
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Ding Q, Ye C. Microbial engineering for shikimate biosynthesis. Enzyme Microb Technol 2023; 170:110306. [PMID: 37598506 DOI: 10.1016/j.enzmictec.2023.110306] [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] [Received: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for chemical synthesis and plant extraction to enhance shikimate biosynthesis, potentially impacting environmental conditions, economic sustainability, and separation and purification processes. Microbial engineering has been developed as an environmentally friendly approach for shikimate biosynthesis. In this review, we provide a comprehensive summary of microbial strategies for shikimate biosynthesis. These strategies primarily include chassis construction, biochemical optimization, pathway remodelling, and global regulation. Furthermore, we discuss future perspectives on shikimate biosynthesis and emphasize the importance of utilizing advanced metabolic engineering tools to regulate microbial networks for constructing robust microbial cell factories.
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Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China; Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
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3
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Ding Q, Ye C. Microbial cell factories based on filamentous bacteria, yeasts, and fungi. Microb Cell Fact 2023; 22:20. [PMID: 36717860 PMCID: PMC9885587 DOI: 10.1186/s12934-023-02025-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved. RESULTS As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains. CONCLUSIONS In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.
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Affiliation(s)
- Qiang Ding
- grid.252245.60000 0001 0085 4987School of Life Sciences, Anhui University, Hefei, 230601 China ,grid.252245.60000 0001 0085 4987Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601 Anhui China ,Anhui Key Laboratory of Modern Biomanufacturing, Hefei, 230601 Anhui China
| | - Chao Ye
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023 China
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4
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Li C, Jiang T, Li M, Zou Y, Yan Y. Fine-tuning gene expression for improved biosynthesis of natural products: From transcriptional to post-translational regulation. Biotechnol Adv 2022; 54:107853. [PMID: 34637919 PMCID: PMC8724446 DOI: 10.1016/j.biotechadv.2021.107853] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/08/2023]
Abstract
Microbial production of natural compounds has attracted extensive attention due to their high value in pharmaceutical, cosmetic, and food industries. Constructing efficient microbial cell factories for biosynthesis of natural products requires the fine-tuning of gene expressions to minimize the accumulation of toxic metabolites, reduce the competition between cell growth and product generation, as well as achieve the balance of redox or co-factors. In this review, we focus on recent advances in fine-tuning gene expression at the DNA, RNA, and protein levels to improve the microbial biosynthesis of natural products. Commonly used regulatory toolsets in each level are discussed, and perspectives for future direction in this area are provided.
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Affiliation(s)
- Chenyi Li
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Tian Jiang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Michelle Li
- North Oconee High School, Bogart, GA 30622, USA
| | - Yusong Zou
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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5
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Wang Z, Doshi A, Chowdhury R, Wang Y, Maranas CD, Cirino PC. Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid. Protein Eng Des Sel 2020; 33:5993570. [DOI: 10.1093/protein/gzaa027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/01/2020] [Accepted: 10/09/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
We previously described the design of triacetic acid lactone (TAL) biosensor ‘AraC-TAL1’, based on the AraC regulatory protein. Although useful as a tool to screen for enhanced TAL biosynthesis, this variant shows elevated background (leaky) expression, poor sensitivity and relaxed inducer specificity, including responsiveness to orsellinic acid (OA). More sensitive biosensors specific to either TAL or OA can aid in the study and engineering of polyketide synthases that produce these and similar compounds. In this work, we employed a TetA-based dual-selection to isolate new TAL-responsive AraC variants showing reduced background expression and improved TAL sensitivity. To improve TAL specificity, OA was included as a ‘decoy’ ligand during negative selection, resulting in the isolation of a TAL biosensor that is inhibited by OA. Finally, to engineer OA-specific AraC variants, the iterative protein redesign and optimization computational framework was employed, followed by 2 rounds of directed evolution, resulting in a biosensor with 24-fold improved OA/TAL specificity, relative to AraC-TAL1.
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Affiliation(s)
- Zhiqing Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
| | - Aarti Doshi
- Department of Biology and Biochemistry, University of Houston, 3507 Cullen Blvd, Houston, TX 77204-5008 Houston, TX, USA
| | - Ratul Chowdhury
- Department of Chemical and Biomedical Engineering, Penn State University, University Park, PA 16802-4400 PA, USA
| | - Yixi Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
| | - Costas D Maranas
- Department of Chemical and Biomedical Engineering, Penn State University, University Park, PA 16802-4400 PA, USA
| | - Patrick C Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Rd, Houston, TX 77204-4004 Houston, TX, USA
- Department of Biology and Biochemistry, University of Houston, 3507 Cullen Blvd, Houston, TX 77204-5008 Houston, TX, USA
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6
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Ting WW, Ng IS. Metabolic manipulation through CRISPRi and gene deletion to enhance cadaverine production in Escherichia coli. J Biosci Bioeng 2020; 130:553-562. [PMID: 32792329 DOI: 10.1016/j.jbiosc.2020.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/01/2020] [Accepted: 07/17/2020] [Indexed: 02/08/2023]
Abstract
Due to the limiting natural resources, greenhouse effect and global warming crisis, the bio-based chemicals which are environmentally friendly materials have gradually become urgent and important. Cadaverine, a 1,5-diaminopentane (DAP), is widely used as block chemicals for synthesis of biopolymer, which can be produced from lysine by lysine decarboxylase (EC 4.1.1.18) in Escherichia coli. However, the DAP will be further utilized into by-products through downstream genes of speE, puuA, speG and ygjG, which decrease the amount of product. In this study, two approaches including Lambda-Red system for gene knockout, and clustered regularly interspaced short palindromic repeats interference (CRISPRi) for gene knockdown; are explored to manipulate the metabolic flux among 26 genetic E. coli. As a result, CadA driven by inducible T7 promoter accumulated more DAP from CRISPRi targeted on single-gene repressive strains such as BT7AiE, BT7AiP, BT7AiG and BT7AiY. The highest DAP titer and productivity was obtained to 38 g/L and 2.67 g/L/h in BT7AiY (repression of ygjG). We also investigated the co-factor pyridoxal 5'-phosphate (PLP) effect on lysine consumption and DAP production from different E. coli derivatives. In contrast to CRISPRi-mediated strains, 4 genes knockout strain (BT7AdEPGY) deal with 98% lysine consumption and achieved 37.45 g/L DAP and 3.17 g/L/h DAP productivity. The metabolic regulation by CRISPRi is a simple strategy and the results are consistent with gene knockout to manipulate the pathway for DAP production.
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Affiliation(s)
- Wan-Wen Ting
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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7
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Kim JW, Lee YG, Kim SJ, Jin YS, Seo JH. Deletion of glycerol-3-phosphate dehydrogenase genes improved 2,3-butanediol production by reducing glycerol production in pyruvate decarboxylase-deficient Saccharomyces cerevisiae. J Biotechnol 2019; 304:31-37. [PMID: 31421146 DOI: 10.1016/j.jbiotec.2019.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/06/2019] [Accepted: 08/14/2019] [Indexed: 01/14/2023]
Abstract
2,3-Butanediol (2,3-BD) can be produced at high titers by engineered Saccharomyces cerevisiae by abolishing the ethanol biosynthetic pathway and introducing the bacterial butanediol-producing pathway. However, production of 2,3-BD instead of ethanol by engineered S. cerevisiae has resulted in glycerol production because of surplus NADH accumulation caused by a lower degree of reduction (γ = 5.5) of 2,3-BD than that (γ = 6) of ethanol. In order to eliminate glycerol production and resolve redox imbalance during 2,3-BD production, both GPD1 and GPD2 coding for glycerol-3-phosphate dehydrogenases were disrupted after overexpressing NADH oxidase from Lactococcus lactis. As disruption of the GPD genes caused growth defects due to limited supply of C2 compounds, Candida tropicalis PDC1 was additionally introduced to provide a necessary amount of C2 compounds while minimizing ethanol production. The resulting strain (BD5_T2 nox_dGPD1,2_CtPDC1) produced 99.4 g/L of 2,3-BD with 0.5 g/L glycerol accumulation in a batch culture. The fed-batch fermentation led to production of 108.6 g/L 2,3-BD with a negligible amount of glycerol production, resulting in a high BD yield (0.462 g2,3-BD/gglucose) corresponding to 92.4 % of the theoretical yield. These results demonstrate that glycerol-free production of 2,3-BD by engineered yeast is feasible.
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Affiliation(s)
- Jin-Woo Kim
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Repubilc of Korea
| | - Ye-Gi Lee
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Repubilc of Korea
| | - Soo-Jung Kim
- Department of Food Science and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61822, USA
| | - Jin-Ho Seo
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Repubilc of Korea.
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Shi YM, Brachmann AO, Westphalen MA, Neubacher N, Tobias NJ, Bode HB. Dual phenazine gene clusters enable diversification during biosynthesis. Nat Chem Biol 2019; 15:331-339. [PMID: 30886436 DOI: 10.1038/s41589-019-0246-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 02/13/2019] [Indexed: 11/10/2022]
Abstract
Biosynthetic gene clusters (BGCs) bridging genotype and phenotype continuously evolve through gene mutations and recombinations to generate chemical diversity. Phenazine BGCs are widespread in bacteria, and the biosynthetic mechanisms of the formation of the phenazine structural core have been illuminated in the last decade. However, little is known about the complex phenazine core-modification machinery. Here, we report the diversity-oriented modifications of the phenazine core through two distinct BGCs in the entomopathogenic bacterium Xenorhabdus szentirmaii, which lives in symbiosis with nematodes. A previously unidentified aldehyde intermediate, which can be modified by multiple enzymatic and non-enzymatic reactions, is a common intermediate bridging the pathways encoded by these BGCs. Evaluation of the antibiotic activity of the resulting phenazine derivatives suggests a highly effective strategy to convert Gram-positive specific phenazines into broad-spectrum antibiotics, which might help the bacteria-nematode complex to maintain its special environmental niche.
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Affiliation(s)
- Yi-Ming Shi
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Alexander O Brachmann
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany.,Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Margaretha A Westphalen
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Nick Neubacher
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Nicholas J Tobias
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany. .,Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany.
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9
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De Paepe B, Maertens J, Vanholme B, De Mey M. Chimeric LysR-Type Transcriptional Biosensors for Customizing Ligand Specificity Profiles toward Flavonoids. ACS Synth Biol 2019; 8:318-331. [PMID: 30563319 DOI: 10.1021/acssynbio.8b00326] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Transcriptional biosensors enable key applications in both metabolic engineering and synthetic biology. Due to nature's immense variety of metabolites, these applications require biosensors with a ligand specificity profile customized to the researcher's needs. In this work, chimeric biosensors were created by introducing parts of a donor regulatory circuit from Sinorhizobium meliloti, delivering the desired luteolin-specific response, into a nonspecific biosensor chassis from Herbaspirillum seropedicae. Two strategies were evaluated for the development of chimeric LysR-type biosensors with customized ligand specificity profiles toward three closely related flavonoids, naringenin, apigenin, and luteolin. In the first strategy, chimeric promoter regions were constructed at the biosensor effector module, while in the second strategy, chimeric transcription factors were created at the biosensor detector module. Via both strategies, the biosensor repertoire was expanded with luteolin-specific chimeric biosensors demonstrating a variety of response curves and ligand specificity profiles. Starting from the nonspecific biosensor chassis, a shift from 27.5% to 95.3% luteolin specificity was achieved with the created chimeric biosensors. Both strategies provide a compelling, faster, and more accessible route for the customization of biosensor ligand specificity, compared to de novo design and construction of each biosensor circuit for every desired ligand specificity.
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Affiliation(s)
- Brecht De Paepe
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University − VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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10
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Tian T, Kang JW, Kang A, Lee TS. Redirecting Metabolic Flux via Combinatorial Multiplex CRISPRi-Mediated Repression for Isopentenol Production in Escherichia coli. ACS Synth Biol 2019; 8:391-402. [PMID: 30681833 DOI: 10.1021/acssynbio.8b00429] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
CRISPR interference (CRISPRi) via target guide RNA (gRNA) arrays and a deactivated Cas9 (dCas9) protein has been shown to simultaneously repress expression of multiple genomic DNA loci. By knocking down endogenous genes in competing pathways, CRISPRi technology can be utilized to redirect metabolic flux toward target metabolite. In this study, we constructed a CRISPRi-mediated multiplex repression system to silence transcription of several endogenous genes to increase precursor availability in a heterologous isopentenol biosynthesis pathway. To identify genomic knockdown targets in competing pathways, we first designed a single-gRNA library with 15 individual targets, where 3 gRNA cassettes targeting gene asnA, prpE, and gldA increased isopentenol titer by 18-24%. We then combined the 3 single-gRNA cassettes into a two- or three-gRNA array and observed up to 98% enhancement in production by fine-tuning the repression level through titrating dCas9 expression. Our strategy shows that multiplex combinatorial knockdown of competing genes using CRISPRi can increase production of the target metabolite, while the repression level needs to be adjusted to balance the metabolic network and achieve the maximum titer improvement.
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Affiliation(s)
- Tian Tian
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jing Wei Kang
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical Engineering, University of California, Berkeley, California 94720, United States
| | - Aram Kang
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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11
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Qian S, Li Y, Cirino PC. Biosensor-guided improvements in salicylate production by recombinant Escherichia coli. Microb Cell Fact 2019; 18:18. [PMID: 30696431 PMCID: PMC6350385 DOI: 10.1186/s12934-019-1069-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/20/2019] [Indexed: 11/10/2022] Open
Abstract
Background Salicylate can be biosynthesized from the common metabolic intermediate shikimate and has found applications in pharmaceuticals and in the bioplastics industry. While much metabolic engineering work focused on the shikimate pathway has led to the biosynthesis of a variety of aromatic compounds, little is known about how the relative expression levels of pathway components influence salicylate biosynthesis. Furthermore, some host strain gene deletions that improve salicylate production may be impossible to predict. Here, a salicylate-responsive transcription factor was used to optimize the expression levels of shikimate/salicylate pathway genes in recombinant E. coli, and to screen a chromosomal transposon insertion library for improved salicylate production. Results A high-throughput colony screen was first developed based on a previously designed salicylate-responsive variant of the E. coli AraC regulatory protein (“AraC-SA”). Next, a combinatorial library was constructed comprising a series of ribosome binding site sequences corresponding to a range of predicted protein translation initiation rates, for each of six pathway genes (> 38,000 strain candidates). Screening for improved salicylate production allowed for the rapid identification of optimal gene expression patterns, conferring up to 123% improved production of salicylate in shake-flask culture. Finally, transposon mutagenesis and screening revealed that deletion of rnd (encoding RNase D) from the host chromosome further improved salicylate production by 27%. Conclusions These results demonstrate the effectiveness of the salicylate sensor-based screening platform to rapidly identify beneficial gene expression patterns and gene knockout targets for improving production. Such customized high-throughput tools complement other cell factory engineering strategies. This approach can be generalized for the production of other shikimate-derived compounds. Electronic supplementary material The online version of this article (10.1186/s12934-019-1069-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuai Qian
- Department of Chemical & Biomolecular Engineering, University of Houston, S222 Engineering Building 1, Houston, TX, 77204-4004, USA
| | - Ye Li
- Department of Chemical & Biomolecular Engineering, University of Houston, S222 Engineering Building 1, Houston, TX, 77204-4004, USA
| | - Patrick C Cirino
- Department of Chemical & Biomolecular Engineering, University of Houston, S222 Engineering Building 1, Houston, TX, 77204-4004, USA.
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12
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History, Current State, and Emerging Applications of Industrial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 173:13-51. [PMID: 30671594 DOI: 10.1007/10_2018_81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The past 150 years have seen remarkable discoveries, rapidly growing biological knowledge, and giant technological leaps providing biotechnological solutions for healthcare, food production, and other societal needs. Genetic engineering, miniaturization, and ever-increasing computing power, in particular, have been key technological drivers for the past few decades. Looking ahead, the eventual transition from fossil resources to biomass and CO2 demands a shift toward a 'bio-economy' based on novel production processes and engineered organisms.
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13
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Frei CS, Qian S, Cirino PC. New engineered phenolic biosensors based on the AraC regulatory protein. Protein Eng Des Sel 2018; 31:213-220. [DOI: 10.1093/protein/gzy024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/24/2018] [Indexed: 01/02/2023] Open
Affiliation(s)
- C S Frei
- Department of Chemical and Biomolecular Engineering, Biocatalysis Laboratory, University of Houston, S337 Engineering Building I, Houston, TX, USA
| | - S Qian
- Department of Chemical and Biomolecular Engineering, Biocatalysis Laboratory, University of Houston, S337 Engineering Building I, Houston, TX, USA
| | - P C Cirino
- Department of Chemical and Biomolecular Engineering, Biocatalysis Laboratory, University of Houston, S337 Engineering Building I, Houston, TX, USA
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Engineering Escherichia coli to increase triacetic acid lactone (TAL) production using an optimized TAL sensor-reporter system. ACTA ACUST UNITED AC 2018; 45:789-793. [DOI: 10.1007/s10295-018-2062-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/13/2018] [Indexed: 12/21/2022]
Abstract
Abstract
Triacetic acid lactone (TAL) (4-hydroxy-6-methyl-2-pyrone) can be upgraded into a variety of higher-value products, and has potential to be developed into a renewable platform chemical through metabolic engineering. We previously developed an endogenous TAL sensor based on the regulatory protein AraC, and applied it to screen 2-pyrone synthase (2-PS) variant libraries in E. coli, resulting in the identification of variants conferring up to 20-fold improved TAL production in liquid culture. In this study, the sensor-reporter system was further optimized and used to further improve TAL production from recombinant E. coli, this time by screening a genomic overexpression library. We identified new and unpredictable gene targets (betT, ompN, and pykA), whose plasmid-based expression improved TAL yield (mg/L/OD595) up to 49% over the control strain. This work further demonstrates the utility of customized transcription factors as molecular reporters in high-throughput engineering of biocatalytic strains.
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15
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Fu R, Martin C, Zhang Y. Next-Generation Plant Metabolic Engineering, Inspired by an Ancient Chinese Irrigation System. MOLECULAR PLANT 2018; 11:47-57. [PMID: 28893713 DOI: 10.1016/j.molp.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/06/2017] [Accepted: 09/01/2017] [Indexed: 05/03/2023]
Abstract
Specialized secondary metabolites serve not only to protect plants against abiotic and biotic challenges, but have also been used extensively by humans to combat diseases. Due to the great importance of medicinal plants for health, we need to find new and sustainable ways to improve the production of the specialized metabolites. In addition to direct extraction, recent progress in metabolic engineering of plants offers an alternative supply option. We argue that metabolic engineering for producing the secondary metabolites in plants may have distinct advantages over microbial production platforms, and thus propose new approaches of plant metabolic engineering, which are inspired by an ancient Chinese irrigation system. Metabolic engineering strategies work at three levels: introducing biosynthetic genes, using transcription factors, and improving metabolic flux including increasing the supply of precursors, energy, and reducing power. In addition, recent progress in biotechnology contributes markedly to better engineering, such as the use of specific promoters and the deletion of competing branch pathways. We propose that next-generation plant metabolic engineering will improve current engineering strategies, for the purpose of producing valuable metabolites in plants on industrial scales.
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Affiliation(s)
- Rao Fu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.
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16
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Yang Y, Wu Y, Hu Y, Wang H, Guo L, Fredrickson JK, Cao B. Harnessing the Periplasm of Bacterial Cells To Develop Biocatalysts for the Biosynthesis of Highly Pure Chemicals. Appl Environ Microbiol 2018; 84:e01693-17. [PMID: 29079618 PMCID: PMC5734034 DOI: 10.1128/aem.01693-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/16/2017] [Indexed: 01/27/2023] Open
Abstract
Although biocatalytic transformation has shown great promise in chemical synthesis, there remain significant challenges in controlling high selectivity without the formation of undesirable by-products. For instance, few attempts to construct biocatalysts for de novo synthesis of pure flavin mononucleotide (FMN) have been successful, due to riboflavin (RF) accumulating in the cytoplasm and being secreted with FMN. To address this problem, we show here a novel biosynthesis strategy, compartmentalizing the final FMN biosynthesis step in the periplasm of an engineered Escherichia coli strain. This construct is able to overproduce FMN with high specificity (92.4% of total excreted flavins). Such a biosynthesis approach allows isolation of the final biosynthesis step from the cytoplasm to eliminate undesirable by-products, providing a new route to develop biocatalysts for the synthesis of high-purity chemicals.IMPORTANCE The periplasm of Gram-negative bacterial hosts is engineered to compartmentalize the final biosynthesis step from the cytoplasm. This strategy is promising for the overproduction of high-value products with high specificity. We demonstrate the successful implementation of this strategy in microbial production of highly pure FMN.
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Affiliation(s)
- Yun Yang
- School of Chemistry and Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, People's Republic of China
| | - Yichao Wu
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Yidan Hu
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Hua Wang
- School of Chemistry and Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, People's Republic of China
| | - Lin Guo
- School of Chemistry and Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, People's Republic of China
| | | | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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17
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Non-protein biologic therapeutics. Curr Opin Biotechnol 2017; 53:65-75. [PMID: 29289799 DOI: 10.1016/j.copbio.2017.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/10/2017] [Accepted: 12/11/2017] [Indexed: 01/15/2023]
Abstract
While the therapeutic biologics are dominated by therapeutic proteins, particularly monoclonal antibodies, a wide range of non-protein therapeutic biologics are rapidly gaining ground both in clinical studies and approved products. Many of these first-in-class therapies provide novel treatment modalities and address previously untreatable conditions or undruggable targets. In particular, novel treatments for rare genetic disorders and qualitatively different oncology therapeutics have been approved in the last two years. This review discusses recent advances in peptide, nucleic acid, carbohydrate, vaccine, and cell-based therapies as well as the manufacturing and commercialization challenges associated with these novel therapeutics.
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18
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Sato-Nakai M, Kawashima K, Nakagawa T, Tachibana Y, Yoshida M, Takanashi K, Morcos PN, Binder M, Moore DJ, Yu L. Metabolites of alectinib in human: their identification and pharmacological activity. Heliyon 2017; 3:e00354. [PMID: 28725874 PMCID: PMC5506877 DOI: 10.1016/j.heliyon.2017.e00354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/21/2017] [Accepted: 07/05/2017] [Indexed: 01/19/2023] Open
Abstract
Two metabolites (M4 and M1b) in plasma and four metabolites (M4, M6, M1a and M1b) in faeces were detected through the human ADME study following a single oral administration of [14C]alectinib, a small-molecule anaplastic lymphoma kinase inhibitor, to healthy subjects. In the present study, M1a and M1b, which chemical structures had not been identified prior to the human ADME study, were identified as isomers of a carboxylate metabolite oxidatively cleaved at the morpholine ring. In faeces, M4 and M1b were the main metabolites, which shows that the biotransformation to M4 and M1b represents two main metabolic pathways for alectinib. In plasma, M4 was a major metabolite and M1b was a minor metabolite. The contribution to in vivo pharmacological activity of these circulating metabolites was assessed from their in vitro pharmacological activity and plasma protein binding. M4 had a similar cancer cell growth inhibitory activity and plasma protein binding to that of alectinib, suggesting its contribution to the antitumor activity of alectinib, whereas the pharmacological activity of M1b was insignificant.
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Affiliation(s)
- Mika Sato-Nakai
- Research division, Chugai Pharmaceuticals, Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Kosuke Kawashima
- Research division, Chugai Pharmaceuticals, Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Toshito Nakagawa
- Research division, Chugai Pharmaceuticals, Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Yukako Tachibana
- Research division, Chugai Pharmaceuticals, Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Miyuki Yoshida
- Research division, Chugai Pharmaceuticals, Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Kenji Takanashi
- Research division, Chugai Pharmaceuticals, Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan
| | - Peter N Morcos
- Roche Innovation Center New York, 430 East 29th Street, New York, NY10016, United States
| | - Martin Binder
- Roche Innovation Center Basel, Knozern-Hauptsitz, Grenzacherstrasse 124, CH-4070, Basel, Switzerland
| | - David J Moore
- Roche Innovation Center New York, 430 East 29th Street, New York, NY10016, United States
| | - Li Yu
- Roche Innovation Center New York, 430 East 29th Street, New York, NY10016, United States
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19
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Wang C, Pfleger BF, Kim SW. Reassessing Escherichia coli as a cell factory for biofuel production. Curr Opin Biotechnol 2017; 45:92-103. [DOI: 10.1016/j.copbio.2017.02.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/05/2017] [Accepted: 02/09/2017] [Indexed: 11/29/2022]
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20
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De Paepe B, Peters G, Coussement P, Maertens J, De Mey M. Tailor-made transcriptional biosensors for optimizing microbial cell factories. J Ind Microbiol Biotechnol 2016; 44:623-645. [PMID: 27837353 DOI: 10.1007/s10295-016-1862-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/30/2016] [Indexed: 12/24/2022]
Abstract
Monitoring cellular behavior and eventually properly adapting cellular processes is key to handle the enormous complexity of today's metabolic engineering questions. Hence, transcriptional biosensors bear the potential to augment and accelerate current metabolic engineering strategies, catalyzing vital advances in industrial biotechnology. The development of such transcriptional biosensors typically starts with exploring nature's richness. Hence, in a first part, the transcriptional biosensor architecture and the various modi operandi are briefly discussed, as well as experimental and computational methods and relevant ontologies to search for natural transcription factors and their corresponding binding sites. In the second part of this review, various engineering approaches are reviewed to tune the main characteristics of these (natural) transcriptional biosensors, i.e., the response curve and ligand specificity, in view of specific industrial biotechnology applications, which is illustrated using success stories of transcriptional biosensor engineering.
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Affiliation(s)
- Brecht De Paepe
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Gert Peters
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Pieter Coussement
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Jo Maertens
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Marjan De Mey
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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