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Lee JY, Cha S, Lee JH, Lim HG, Noh MH, Kang CW, Jung GY. Plug-in repressor library for precise regulation of metabolic flux in Escherichia coli. Metab Eng 2021; 67:365-372. [PMID: 34333137 DOI: 10.1016/j.ymben.2021.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
In metabolic engineering, enhanced production of value-added chemicals requires precise flux control between growth-essential competing and production pathways. Although advances in synthetic biology have facilitated the exploitation of a number of genetic elements for precise flux control, their use requires expensive inducers, or more importantly, needs complex and time-consuming processes to design and optimize appropriate regulator components, case-by-case. To overcome this issue, we devised the plug-in repressor libraries for target-specific flux control, in which expression levels of the repressors were diversified using degenerate 5' untranslated region (5' UTR) sequences employing the UTR Library Designer. After we validated a wide expression range of the repressor libraries, they were applied to improve the production of lycopene from glucose and 3-hydroxypropionic acid (3-HP) from acetate in Escherichia coli via precise flux rebalancing to enlarge precursor pools. Consequently, we successfully achieved optimal carbon fluxes around the precursor nodes for efficient production. The most optimized strains were observed to produce 2.59 g/L of 3-HP and 11.66 mg/L of lycopene, which were improved 16.5-fold and 2.82-fold, respectively, compared to those produced by the parental strains. These results indicate that carbon flux rebalancing using the plug-in library is a powerful strategy for efficient production of value-added chemicals in E. coli.
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Affiliation(s)
- Ji Yeon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Sanghak Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Ji Hoon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea.
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Leite EL, Gautron A, Deplanche M, Nicolas A, Ossemond J, Nguyen MT, do Carmo FLR, Gilot D, Azevedo V, Goetz F, Le Loir Y, Otto M, Berkova N. Involvement of caspase-1 in inflammasomes activation and bacterial clearance in S. aureus-infected osteoblast-like MG-63 cells. Cell Microbiol 2020; 22:e13204. [PMID: 32176433 PMCID: PMC10988652 DOI: 10.1111/cmi.13204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/25/2020] [Accepted: 03/05/2020] [Indexed: 12/27/2022]
Abstract
Staphylococcus aureus, a versatile Gram-positive bacterium, is the main cause of bone and joint infections (BJI), which are prone to recurrence. The inflammasome is an immune signaling platform that assembles after pathogen recognition. It activates proteases, most notably caspase-1 that proteolytically matures and promotes the secretion of mature IL-1β and IL-18. The role of inflammasomes and caspase-1 in the secretion of mature IL-1β and in the defence of S. aureus-infected osteoblasts has not yet been fully investigated. We show here that S. aureus-infected osteoblast-like MG-63 but not caspase-1 knock-out CASP1 -/- MG-63 cells, which were generated using CRISPR-Cas9 technology, activate the inflammasome as monitored by the release of mature IL-1β. The effect was strain-dependent. The use of S. aureus deletion and complemented phenole soluble modulins (PSMs) mutants demonstrated a key role of PSMs in inflammasomes-related IL-1β production. Furthermore, we found that the lack of caspase-1 in CASP1 -/- MG-63 cells impairs their defense functions, as bacterial clearance was drastically decreased in CASP1 -/- MG-63 compared to wild-type cells. Our results demonstrate that osteoblast-like MG-63 cells play an important role in the immune response against S. aureus infection through inflammasomes activation and establish a crucial role of caspase-1 in bacterial clearance.
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Affiliation(s)
- Elma Lima Leite
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253 STLO, Rennes, France; Agrocampus Ouest, Unité Mixtes de Recherche 1253 STLO, Rennes, France
- Instituto de Ciências Biológicas - Universidade Federal de Minas Gerais, Belo Horizonte- Minas Gerais, Brazil
| | - Arthur Gautron
- Univ Rennes, CNRS, IGDR [(Institut de génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France
| | - Martine Deplanche
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253 STLO, Rennes, France; Agrocampus Ouest, Unité Mixtes de Recherche 1253 STLO, Rennes, France
| | - Aurelie Nicolas
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253 STLO, Rennes, France; Agrocampus Ouest, Unité Mixtes de Recherche 1253 STLO, Rennes, France
| | - Jordane Ossemond
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253 STLO, Rennes, France; Agrocampus Ouest, Unité Mixtes de Recherche 1253 STLO, Rennes, France
| | - Minh Thu Nguyen
- Paul-Ehrlich-Institute, Federal Regulatory Agency for Vaccines and Biomedicines, Langen 63225, Germany
| | - Fillipe L. R. do Carmo
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253 STLO, Rennes, France; Agrocampus Ouest, Unité Mixtes de Recherche 1253 STLO, Rennes, France
- Instituto de Ciências Biológicas - Universidade Federal de Minas Gerais, Belo Horizonte- Minas Gerais, Brazil
| | - David Gilot
- Univ Rennes, CNRS, IGDR [(Institut de génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France
| | - Vasco Azevedo
- Instituto de Ciências Biológicas - Universidade Federal de Minas Gerais, Belo Horizonte- Minas Gerais, Brazil
| | - Friedrich Goetz
- Mikrobielle Genetik, Universität Tübingen, D-72076 Tübingen, Germany
| | - Yves Le Loir
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253 STLO, Rennes, France; Agrocampus Ouest, Unité Mixtes de Recherche 1253 STLO, Rennes, France
| | - Michael Otto
- Laboratory of Human Bacterial Pathogenesis, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Nadia Berkova
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1253 STLO, Rennes, France; Agrocampus Ouest, Unité Mixtes de Recherche 1253 STLO, Rennes, France
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Kim B, Kim HJ, Lee SJ. Regulation of Microbial Metabolic Rates Using CRISPR Interference With Expanded PAM Sequences. Front Microbiol 2020; 11:282. [PMID: 32184769 PMCID: PMC7058998 DOI: 10.3389/fmicb.2020.00282] [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: 10/07/2019] [Accepted: 02/07/2020] [Indexed: 12/20/2022] Open
Abstract
Genome-editing CRISPR/Cas9 technology has led to the development of artificial transcriptional repressors, also known as CRISPR interference (CRISPRi). The deactivated Cas9 (dCas9) protein guided by crRNA can specifically bind to target DNA sequences, including promoters and operators, without DNA cleavage. Protospacer adjacent motif (PAM) sequence dependence may be disadvantageous in the design of target-specific CRISPRi, as the PAM sequence is essential for DNA cleavage by the CRISPR/Cas9 system. We constructed a chromosomally integrated dCas9 system (ΔaraBAD:dcas9) in Escherichia coli under the control of the L-arabinose-inducible P BAD promoter. Plasmids carrying various crRNAs with target sequences specific for the gal promoter (-10 region), and the galETK structural genes in the gal operon, were transformed into dCas9-expressing E. coli. Cellular growth and/or galactose metabolic rates were monitored in the presence or absence of gratuitous L-arabinose. D-galactose consumption and cell growth rates were partially retarded by targeting transcriptional elongation but were fully inhibited by targeting transcriptional initiation. Moreover, RT-qPCR analysis showed that CRISPRi with several modified PAM sequences can repress the transcription of target DNAs. These results indicate that cellular metabolic rates and cell growth can be controlled by targeting structural genes or regulatory regions using CRISPRi; also, a loose PAM sequence dependence can expand the DNA targets of CRISPRi.
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Affiliation(s)
- Bumjoon Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
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A Role for the VPS Retromer in Brucella Intracellular Replication Revealed by Genomewide siRNA Screening. mSphere 2019; 4:4/3/e00380-19. [PMID: 31243080 PMCID: PMC6595151 DOI: 10.1128/msphere.00380-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Brucella, the agent causing brucellosis, is a major zoonotic pathogen with worldwide distribution. Brucella resides and replicates inside infected host cells in membrane-bound compartments called Brucella-containing vacuoles (BCVs). Following uptake, Brucella resides in endosomal BCVs (eBCVs) that gradually mature from early to late endosomal features. Through a poorly understood process that is key to the intracellular lifestyle of Brucella, the eBCV escapes fusion with lysosomes by transitioning to the replicative BCV (rBCV), a replicative niche directly connected to the endoplasmic reticulum (ER). Despite the notion that this complex intracellular lifestyle must depend on a multitude of host factors, a holistic view on which of these components control Brucella cell entry, trafficking, and replication is still missing. Here we used a systematic cell-based small interfering RNA (siRNA) knockdown screen in HeLa cells infected with Brucella abortus and identified 425 components of the human infectome for Brucella infection. These include multiple components of pathways involved in central processes such as the cell cycle, actin cytoskeleton dynamics, or vesicular trafficking. Using assays for pathogen entry, knockdown complementation, and colocalization at single-cell resolution, we identified the requirement of the VPS retromer for Brucella to escape the lysosomal degradative pathway and to establish its intracellular replicative niche. We thus validated the VPS retromer as a novel host factor critical for Brucella intracellular trafficking. Further, our genomewide data shed light on the interplay between central host processes and the biogenesis of the Brucella replicative niche.IMPORTANCE With >300,000 new cases of human brucellosis annually, Brucella is regarded as one of the most important zoonotic bacterial pathogens worldwide. The agent causing brucellosis resides inside host cells within vacuoles termed Brucella-containing vacuoles (BCVs). Although a few host components required to escape the degradative lysosomal pathway and to establish the ER-derived replicative BCV (rBCV) have already been identified, the global understanding of this highly coordinated process is still partial, and many factors remain unknown. To gain deeper insight into these fundamental questions, we performed a genomewide RNA interference (RNAi) screen aiming at discovering novel host factors involved in the Brucella intracellular cycle. We identified 425 host proteins that contribute to Brucella cellular entry, intracellular trafficking, and replication. Together, this study sheds light on previously unknown host pathways required for the Brucella infection cycle and highlights the VPS retromer components as critical factors for the establishment of the Brucella intracellular replicative niche.
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Immunologic Pathways in Protective versus Maladaptive Host Responses to Attenuated and Pathogenic Strains of Mycoplasma gallisepticum. Infect Immun 2019; 87:IAI.00613-18. [PMID: 30559221 DOI: 10.1128/iai.00613-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/20/2018] [Indexed: 01/06/2023] Open
Abstract
Mycoplasmas are small bacterial commensals or pathogens that commonly colonize host mucosal tissues and avoid rapid clearance, in part by stimulating inflammatory, immunopathogenic responses. We previously characterized a wide array of transcriptomic perturbations in avian host tracheal mucosae infected with virulent, immunopathologic Mycoplasma gallisepticum; however, mechanisms delineating these from protective responses, such as those induced upon vaccination, have not been thoroughly explored. In this study, host transcriptomic responses to two experimental M. gallisepticum vaccines were assessed during the first 2 days of infection. Relative to virulent infection, host metabolic and immune gene responses to both vaccines were greatly decreased, including early innate immune responses critical to disease development and subsequent adaptive immunity. These data specify host genes and potential mechanisms contributing to maladaptive versus beneficial host responses-information critical for design of vaccines efficacious in both limiting inflammation and enabling pathogen clearance.
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Drug combinations: a strategy to extend the life of antibiotics in the 21st century. Nat Rev Microbiol 2019; 17:141-155. [PMID: 30683887 DOI: 10.1038/s41579-018-0141-x] [Citation(s) in RCA: 436] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/22/2018] [Indexed: 01/03/2023]
Abstract
Antimicrobial resistance threatens a resurgence of life-threatening bacterial infections and the potential demise of many aspects of modern medicine. Despite intensive drug discovery efforts, no new classes of antibiotics have been developed into new medicines for decades, in large part owing to the stringent chemical, biological and pharmacological requisites for effective antibiotic drugs. Combinations of antibiotics and of antibiotics with non-antibiotic activity-enhancing compounds offer a productive strategy to address the widespread emergence of antibiotic-resistant strains. In this Review, we outline a theoretical and practical framework for the development of effective antibiotic combinations.
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