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Li S, Ye Z, Moreb EA, Menacho-Melgar R, Golovsky M, Lynch MD. 2-Stage microfermentations. Metab Eng Commun 2024; 18:e00233. [PMID: 38665924 PMCID: PMC11043886 DOI: 10.1016/j.mec.2024.e00233] [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] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Cell based factories can be engineered to produce a wide variety of products. Advances in DNA synthesis and genome editing have greatly simplified the design and construction of these factories. It has never been easier to generate hundreds or even thousands of cell factory strain variants for evaluation. These advances have amplified the need for standardized, higher throughput means of evaluating these designs. Toward this goal, we have previously reported the development of engineered E. coli strains and associated 2-stage production processes to simplify and standardize strain engineering, evaluation and scale up. This approach relies on decoupling growth (stage 1), from production, which occurs in stationary phase (stage 2). Phosphate depletion is used as the trigger to stop growth as well as induce heterologous expression. Here, we describe in detail the development of protocols for the evaluation of engineered E. coli strains in 2-stage microfermentations. These protocols are readily adaptable to the evaluation of strains producing a wide variety of protein as well as small molecule products. Additionally, by detailing the approach to protocol development, these methods are also adaptable to additional cellular hosts, as well as other 2-stage processes with various additional triggers.
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Affiliation(s)
- Shuai Li
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Eirik A. Moreb
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | | | - Michael D. Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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Jiang X, Shu H, Feng S, Wang P, Zhang Z, Wang N. A Hadal Streptomyces-Derived Echinocandin Acylase Discovered through the Prioritization of Protein Families. Mar Drugs 2024; 22:212. [PMID: 38786603 PMCID: PMC11122479 DOI: 10.3390/md22050212] [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: 04/04/2024] [Revised: 04/28/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Naturally occurring echinocandin B and FR901379 are potent antifungal lipopeptides featuring a cyclic hexapeptide nucleus and a fatty acid side chain. They are the parent compounds of echinocandin drugs for the treatment of severe fungal infections caused by the Candida and Aspergilla species. To minimize hemolytic toxicity, the native fatty acid side chains in these drug molecules are replaced with designer acyl side chains. The deacylation of the N-acyl side chain is, therefore, a crucial step for the development and manufacturing of echinocandin-type antibiotics. Echinocandin E (ECE) is a novel echinocandin congener with enhanced stability generated via the engineering of the biosynthetic machinery of echinocandin B (ECB). In the present study, we report the discovery of the first echinocandin E acylase (ECEA) using the enzyme similarity tool (EST) for enzymatic function mining across protein families. ECEA is derived from Streptomyces sp. SY1965 isolated from a sediment collected from the Mariana Trench. It was cloned and heterologously expressed in S. lividans TK24. The resultant TKecea66 strain showed efficient cleavage activity of the acyl side chain of ECE, showing promising applications in the development of novel echinocandin-type therapeutics. Our results also provide a showcase for harnessing the essentially untapped biodiversity from the hadal ecosystems for the discovery of functional molecules.
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Affiliation(s)
- Xuejian Jiang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (X.J.); (H.S.); (S.F.); (P.W.); (Z.Z.)
| | - Hongjun Shu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (X.J.); (H.S.); (S.F.); (P.W.); (Z.Z.)
| | - Shuting Feng
- Ocean College, Zhejiang University, Zhoushan 316021, China; (X.J.); (H.S.); (S.F.); (P.W.); (Z.Z.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (X.J.); (H.S.); (S.F.); (P.W.); (Z.Z.)
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Zhizhen Zhang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (X.J.); (H.S.); (S.F.); (P.W.); (Z.Z.)
| | - Nan Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (X.J.); (H.S.); (S.F.); (P.W.); (Z.Z.)
- Hainan Institute of Zhejiang University, Sanya 572025, China
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3
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Inciuraite R, Gedgaudas R, Lukosevicius R, Tilinde D, Ramonaite R, Link A, Kasetiene N, Malakauskas M, Kiudelis G, Jonaitis LV, Kupcinskas J, Juzenas S, Skieceviciene J. Constituents of stable commensal microbiota imply diverse colonic epithelial cell reactivity in patients with ulcerative colitis. Gut Pathog 2024; 16:16. [PMID: 38521943 PMCID: PMC10960424 DOI: 10.1186/s13099-024-00612-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Despite extensive research on microbiome alterations in ulcerative colitis (UC), the role of the constituent stable microbiota remains unclear. RESULTS This study, employing 16S rRNA-gene sequencing, uncovers a persistent microbial imbalance in both active and quiescent UC patients compared to healthy controls. Using co-occurrence and differential abundance analysis, the study highlights microbial constituents, featuring Phocaeicola, Collinsella, Roseburia, Holdemanella, and Bacteroides, that are not affected during the course of UC. Co-cultivation experiments, utilizing commensal Escherichia coli and Phocaeicola vulgatus, were conducted with intestinal epithelial organoids derived from active UC patients and controls. These experiments reveal a tendency for a differential response in tight junction formation and maintenance in colonic epithelial cells, without inducing pathogen recognition and stress responses, offering further insights into the roles of these microorganisms in UC pathogenesis. These experiments also uncover high variation in patients' response to the same bacteria, which indicate the need for more comprehensive, stratified analyses with an expanded sample size. CONCLUSION This study reveals that a substantial part of the gut microbiota remains stable throughout progression of UC. Functional experiments suggest that members of core microbiota - Escherichia coli and Phocaeicola vulgatus - potentially differentially regulate the expression of tight junction gene in the colonic epithelium of UC patients and healthy individuals.
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Affiliation(s)
- Ruta Inciuraite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania.
| | - Rolandas Gedgaudas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Deimante Tilinde
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rima Ramonaite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital Magdeburg, Magdeburg, Germany
| | - Neringa Kasetiene
- Department of Food Safety and Quality, Academy of Veterinary, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Mindaugas Malakauskas
- Department of Food Safety and Quality, Academy of Veterinary, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Gediminas Kiudelis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Laimas Virginijus Jonaitis
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Simonas Juzenas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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Soma Y, Tominaga S, Tokito K, Imado Y, Naka K, Hanai T, Takahashi M, Izumi Y, Bamba T. Trace impurities in sodium phosphate influences the physiological activity of Escherichia coli in M9 minimal medium. Sci Rep 2023; 13:17396. [PMID: 37833342 PMCID: PMC10576033 DOI: 10.1038/s41598-023-44526-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of applied microbiology, reproducibility and experimental variability are important factors that influence both basic research as well as process development for industrial applications. Experimental reproducibility and accuracy depend not only on culture conditions such as temperature and aeration but also on raw materials and procedures used for media preparation. The M9 minimal medium is one of the most common synthetic media for culturing Escherichia coli and other bacteria. This synthetic medium can be used to observe and evaluate the physiological activity of microbes under minimal nutritional requirements and determine the limiting factor for the desired phenotype. Although one of the advantages using the M9 medium is that its composition can be modulated, it is difficult to control presence of trace components and impurities from the reagents for preparing this medium. Herein, we showed that trace ingredients present in the reagents used for M9 media preparation affect the bacterial physiological activities (e.g., cell growth, substrate consumption, and byproduct formation). Additionally, we systematically identified the trace ingredient that influenced phenotypic differences. Our results showed that the selection of reagents and accuracy during reagent preparation is important for experimental reproducibility in the field of bio-engineering and systems biology focused on the systematic and continuous development of biomolecular systems (e.g., biorefinery, metabolic engineering, and synthetic biology).
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Affiliation(s)
- Yuki Soma
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
- Laboratory for Synthetic Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, W5-729, 819-0395, Japan
| | - Saki Tominaga
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kanako Tokito
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yuri Imado
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kosuke Naka
- Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Taizo Hanai
- Laboratory for Synthetic Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, W5-729, 819-0395, Japan
| | - Masatomo Takahashi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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Novoskoltseva OA, Litmanovich EA, Loiko NG, Nikolaev YA, Yaroslavov AA. Biodegradable Water-Soluble Matrix for Immobilization of Biocidal 4-Hexylresorcinol. Int J Mol Sci 2023; 24:14717. [PMID: 37834163 PMCID: PMC10572309 DOI: 10.3390/ijms241914717] [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: 09/01/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Biocidal coatings have been used in biomedicine, cosmetology and the food industry. In this article, the coatings are described as being composed of non-stoichiometric polycomplexes, products of electrostatic coupling of two commercial biodegradable ionic polymers, anionic sodium alginate and cationic quaternized hydroxyethyl cellulose ethoxylate. Non-stoichiometric polycomplexes with a 5-fold excess of the cationic polymer were used for immobilizing hydrophobic biocidal 4-hexylresorcinol (HR). Being dispersed in water, the polycomplex particles were capable of absorbing a tenfold excess of HR in relation to the polycation. After deposition onto the plastic surface and drying, the aqueous polycomplex-HR composite formulation forms a transparent homogeneous coating, which swells slightly in water. The interpolyelectrolyte complex (IPEC) is substantially non-toxic. The incorporation of HR in the IPEC imparts antimicrobial activity to the resulting composite, in both aqueous solutions and coatings, against Gram-negative and Gram-positive bacteria and yeast. The polysaccharide-based polycomplexes with embedded HR are promising for the fabrication of biocidal films and coatings.
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Affiliation(s)
- Olga A. Novoskoltseva
- Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.N.); (E.A.L.)
| | - Ekaterina A. Litmanovich
- Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.N.); (E.A.L.)
| | - Nataliya G. Loiko
- Department of Microbiology, Federal Research Center “Fundamentals of Biotechnology” RAS, 119071 Moscow, Russia; (N.G.L.); (Y.A.N.)
| | - Yury A. Nikolaev
- Department of Microbiology, Federal Research Center “Fundamentals of Biotechnology” RAS, 119071 Moscow, Russia; (N.G.L.); (Y.A.N.)
| | - Alexander A. Yaroslavov
- Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.N.); (E.A.L.)
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Sikkema AP, Tabatabaei SK, Lee YJ, Lund S, Lohman GJS. High-Complexity One-Pot Golden Gate Assembly. Curr Protoc 2023; 3:e882. [PMID: 37755329 DOI: 10.1002/cpz1.882] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Golden Gate Assembly is a flexible method of DNA assembly and cloning that permits the joining of multiple fragments in a single reaction through predefined connections. The method depends on cutting DNA using a Type IIS restriction enzyme, which cuts outside its recognition site and therefore can generate overhangs of any sequence while separating the recognition site from the generated fragment. By choosing compatible fusion sites, Golden Gate permits the joining of multiple DNA fragments in a defined order in a single reaction. Conventionally, this method has been used to join five to eight fragments in a single assembly round, with yield and accuracy dropping off rapidly for more complex assemblies. Recently, we demonstrated the application of comprehensive measurements of ligation fidelity and bias data using data-optimized assembly design (DAD) to enable a high degree of assembly accuracy for very complex assemblies with the simultaneous joining of as many as 52 fragments in one reaction. Here, we describe methods for applying DAD principles and online tools to evaluate the fidelity of existing fusion site sets and assembly standards, selecting new optimal sets, and adding fusion sites to existing assemblies. We further describe the application of DAD to divide known sequences at optimal points, including designing one-pot assemblies of small genomes. Using the T7 bacteriophage genome as an example, we present a protocol that includes removal of native Type IIS sites (domestication) simultaneously with parts generation by PCR. Finally, we present recommended cycling protocols for assemblies of medium to high complexity (12-36 fragments), methods for producing high-quality parts, examples highlighting the importance of DNA purity and fragment stoichiometric balance for optimal assembly outcomes, and methods for assessing assembly success. © 2023 New England Biolabs, Inc. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assessing the fidelity of an overhang set using the NEBridge Ligase Fidelity Viewer Basic Protocol 2: Generating a high-fidelity overhang set using the NEBridge GetSet Tool Alternate Protocol 1: Expanding an existing overhang set using the NEBridge GetSet Tool Basic Protocol 3: Dividing a genomic sequence with optimal fusion sites using the NEBridge SplitSet Tool Basic Protocol 4: One-pot Golden Gate Assembly of 12 fragments into a destination plasmid Alternate Protocol 2: One-pot Golden Gate Assembly of 24+ fragments into a destination plasmid Basic Protocol 5: One-pot Golden Gate Assembly of the T7 bacteriophage genome from 12+ parts Support Protocol 1: Generation of high-purity amplicons for assembly Support Protocol 2: Cloning assembly parts into a holding vector Support Protocol 3: Quantifying DNA concentration using a Qubit 4 fluorometer Support Protocol 4: Visualizing large assemblies via TapeStation Support Protocol 5: Validating phage genome assemblies via ONT long-read sequencing.
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Affiliation(s)
- Andrew P Sikkema
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
| | | | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
| | - Sean Lund
- Research Department, New England Biolabs, Ipswich, Massachusetts, USA
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Wei Y, Wang T, Wang Y, Zeng S, Ho YP, Ho HP. Rapid Prototyping of Multi-Functional and Biocompatible Parafilm ®-Based Microfluidic Devices by Laser Ablation and Thermal Bonding. MICROMACHINES 2023; 14:mi14030656. [PMID: 36985063 PMCID: PMC10054776 DOI: 10.3390/mi14030656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 05/27/2023]
Abstract
In this paper, we report a simple, rapid, low-cost, biocompatible, and detachable microfluidic chip fabrication method for customized designs based on Parafilm®. Here, Parafilm® works as both a bonding agent and a functional membrane. Its high ultimate tensile stress (3.94 MPa) allows the demonstration of high-performance actuators such as microvalves and micropumps. By laser ablation and the one-step bonding of multiple layers, 3D structured microfluidic chips were successfully fabricated within 2 h. The consumption time of this method (~2 h) was 12 times less than conventional photolithography (~24 h). Moreover, the shear stress of the PMMA-Parafilm®-PMMA specimens (0.24 MPa) was 2.13 times higher than that of the PDMS-PDMS specimens (0.08 MPa), and 0.56 times higher than that of the PDMS-Glass specimens (0.16 MPa), showing better stability and reliability. In this method, multiple easily accessible materials such as polymethylmethacrylate (PMMA), PVC, and glass slides were demonstrated and well-incorporated as our substrates. Practical actuation devices that required high bonding strength including microvalves and micropumps were fabricated by this method with high performance. Moreover, the biocompatibility of the Parafilm®-based microfluidic devices was validated through a seven-day E. coli cultivation. This reported fabrication scheme will provide a versatile platform for biochemical applications and point-of-care diagnostics.
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Affiliation(s)
- Yuanyuan Wei
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Tianle Wang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Yuye Wang
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shuwen Zeng
- XLIM Research Institute, UMR 7252, University of Limoges, 123 Avenue Albert Thomas, 87060 Limoges, France
- Light, Nanomaterials & Nanotechnologies (L2n), CNRS-ERL 7004, Université de Technologie de Troyes, 10000 Troyes, France
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
- Centre for Biomaterials, The Chinese University of Hong Kong, Hong Kong 999077, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, Hong Kong 999077, China
- The Ministry of Education Key Laboratory of Regeneration Medicine, Hong Kong 999077, China
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
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Heterologous Expression of Recombinant Human Cytochrome P450 (CYP) in Escherichia coli: N-Terminal Modification, Expression, Isolation, Purification, and Reconstitution. BIOTECH 2023; 12:biotech12010017. [PMID: 36810444 PMCID: PMC9944785 DOI: 10.3390/biotech12010017] [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: 01/03/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Cytochrome P450 (CYP) enzymes play important roles in metabolising endogenous and xenobiotic substances. Characterisations of human CYP proteins have been advanced with the rapid development of molecular technology that allows heterologous expression of human CYPs. Among several hosts, bacteria systems such as Escherichia coli (E. coli) have been widely used thanks to their ease of use, high level of protein yields, and affordable maintenance costs. However, the levels of expression in E. coli reported in the literature sometimes differ significantly. This paper aims to review several contributing factors, including N-terminal modifications, co-expression with a chaperon, selections of vectors and E. coli strains, bacteria culture and protein expression conditions, bacteria membrane preparations, CYP protein solubilizations, CYP protein purifications, and reconstitution of CYP catalytic systems. The common factors that would most likely lead to high expression of CYPs were identified and summarised. Nevertheless, each factor may still require careful evaluation for individual CYP isoforms to achieve a maximal expression level and catalytic activity. Recombinant E. coli systems have been evidenced as a useful tool in obtaining the ideal level of human CYP proteins, which ultimately allows for subsequent characterisations of structures and functions.
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9
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Thomason LC, Costantino N, Li X, Court DL. Recombineering: Genetic Engineering in Escherichia coli Using Homologous Recombination. Curr Protoc 2023; 3:e656. [PMID: 36779782 PMCID: PMC10037674 DOI: 10.1002/cpz1.656] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using either PCR products or synthetic double-stranded DNA (dsDNA) or single-stranded DNA as substrates. Multiple linear dsDNA molecules can be assembled into an intact plasmid. The technology of recombineering is possible because bacteriophage-encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to the location of restriction sites and can also be used in combination with CRISPR/Cas targeting systems. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: Making electrocompetent cells and transforming with linear DNA Support Protocol 1: Selection/counter-selections for genome engineering Support Protocol 2: Creating and screening for oligo recombinants by PCR Support Protocol 3: Other methods of screening for unselected recombinants Support Protocol 4: Curing recombineering plasmids containing a temperature-sensitive replication function Support Protocol 5: Removal of the prophage by recombineering Alternate Protocol 1: Using CRISPR/Cas9 as a counter-selection following recombineering Alternate Protocol 2: Assembly of linear dsDNA fragments into functional plasmids Alternate Protocol 3: Retrieval of alleles onto a plasmid by gap repair Alternate Protocol 4: Modifying multicopy plasmids with recombineering Support Protocol 6: Screening for unselected plasmid recombinants Alternate Protocol 5: Recombineering with an intact λ prophage Alternate Protocol 6: Targeting an infecting λ phage with the defective prophage strains.
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Affiliation(s)
- Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Nina Costantino
- formerly with Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Xintian Li
- Armata Pharmaceuticals, 4503 Glencoe Avenue, Marina del Rey, CA 90292
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
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Ali Q, Ma S, Farooq U, Niu J, Li F, Li D, Wang Z, Sun H, Cui Y, Shi Y. Pasture intake protects against commercial diet-induced lipopolysaccharide production facilitated by gut microbiota through activating intestinal alkaline phosphatase enzyme in meat geese. Front Immunol 2022; 13:1041070. [PMID: 36569878 PMCID: PMC9774522 DOI: 10.3389/fimmu.2022.1041070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Diet strongly affects gut microbiota composition, and gut bacteria can influence the intestinal barrier functions and systemic inflammation through metabolic endotoxemia. In-house feeding system (IHF, a low dietary fiber source) may cause altered cecal microbiota composition and inflammatory responses in meat geese via increased endotoxemia (lipopolysaccharides) with reduced intestinal alkaline phosphatase (ALP) production. The effects of artificial pasture grazing system (AGF, a high dietary fiber source) on modulating gut microbiota architecture and gut barrier functions have not been investigated in meat geese. Therefore, this study aimed to investigate whether intestinal ALP could play a critical role in attenuating reactive oxygen species (ROS) generation and ROS facilitating NF-κB pathway-induced systemic inflammation in meat geese. Methods The impacts of IHF and AGF systems on gut microbial composition via 16 sRNA sequencing were assessed in meat geese. The host markers analysis through protein expression of serum and cecal tissues, hematoxylin and eosin (H&E) staining, localization of NF-қB and Nrf2 by immunofluorescence analysis, western blotting analysis of ALP, and quantitative PCR of cecal tissues was evaluated. Results and Discussion In the gut microbiota analysis, meat geese supplemented with pasture showed a significant increase in commensal microbial richness and diversity compared to IHF meat geese demonstrating the antimicrobial, antioxidant, and anti-inflammatory ability of the AGF system. A significant increase in intestinal ALP-induced Nrf2 signaling pathway was confirmed representing LPS dephosphorylation mediated TLR4/MyD88 induced ROS reduction mechanisms in AGF meat geese. Further, the correlation analysis of top 44 host markers with gut microbiota showed that artificial pasture intake protected gut barrier functions via reducing ROS-mediated NF-κB pathway-induced gut permeability, systemic inflammation, and aging phenotypes. In conclusion, the intestinal ALP functions to regulate gut microbial homeostasis and barrier function appear to inhibit pro-inflammatory cytokines by reducing LPS-induced ROS production in AGF meat geese. The AGF system may represent a novel therapy to counteract the chronic inflammatory state leading to low dietary fiber-related diseases in animals.
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Affiliation(s)
- Qasim Ali
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Sen Ma
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China,Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Henan Agricultural University, Zhengzhou, Henan, China,Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, Henan, China
| | - Umar Farooq
- Department of Poultry Science, University of Agriculture Faisalabad, Toba Tek Singh, Pakistan
| | - Jiakuan Niu
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Fen Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Defeng Li
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China,Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Henan Agricultural University, Zhengzhou, Henan, China,Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhichang Wang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China,Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Henan Agricultural University, Zhengzhou, Henan, China,Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, Henan, China
| | - Hao Sun
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China,Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Henan Agricultural University, Zhengzhou, Henan, China,Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yalei Cui
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China,Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Henan Agricultural University, Zhengzhou, Henan, China,Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yinghua Shi
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China,Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Henan Agricultural University, Zhengzhou, Henan, China,Henan Herbage Engineering Technology Research Center, Henan Agricultural University, Zhengzhou, Henan, China,*Correspondence: Yinghua Shi,
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11
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Biodegradable Interpolycomplexes for Anti-Erosion Stabilization of Soil and Sand. Polymers (Basel) 2022; 14:polym14245383. [PMID: 36559750 PMCID: PMC9786215 DOI: 10.3390/polym14245383] [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: 11/11/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
A linear anionic polysaccharide, sodium alginate, electrostatically interacts with a cationic polysaccharide, quaternized hydroxyethyl cellulose ethoxylate, in aqueous solution, thus giving an interpolyelectrolyte complex. Aqueous solutions of the initial polysaccharides and polycomplexes with an excess of the cationic or anionic polymers were used for the stabilization of soil and sand against water erosion. Physicochemical, mechanical and biological properties of the polymers and coatings were characterized by gravimetric analysis, viscosimetry, mechanical strength assessment, cell viability, and cell-mediated degradation with the following main conclusions. (a) Non-stoichiometric polycomplexes with an excess of cationic or anionic units ("cationic" and "anionic" polycomplexes, respectively) form transparent solutions or stable-in-time dispersions. (b) The complexation results in a decrease in the viscosity of polymer solutions. (c) A complete dissociation of polycomplexes to the initial components is achieved in a 0.2 M NaCl solution. (d) Soil/sand treatment with 1 wt% aqueous solutions of polymers or polycomplexes and further drying lead to the formation of strong composite coatings from polymer(s) and soil/sand particles. (e) Cationic polycomplexes form stronger coatings in comparison with anionic polycomplexes. (f) The polymer-soil coatings are stable towards re-watering, while the polymer-sand coatings show a much lower resistance to water. (g) The individual polysaccharides demonstrate a negligible toxicity to Gram-negative and Gram-positive bacteria and yeast. (h) The addition of Bacillus subtilis culture initiates the degradation of the polysaccharides and polycomplexes. (i) Films from polysaccharides and polycomplexes decompose down to small fragments after being in soil for 6 weeks. The results of the work are of importance for constructing water-resistant, low toxicity and biodegradable protective coatings for soil and sand.
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12
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Vaughan AL, Altermann E, Glare TR, Hurst MRH. Genome sequence of the entomopathogenic Serratia entomophila isolate 626 and characterisation of the species specific itaconate degradation pathway. BMC Genomics 2022; 23:728. [PMID: 36303123 DOI: 10.1186/s12864-022-08938-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Isolates of Serratia entomophila and S. proteamaculans (Yersiniaceae) cause disease specific to the endemic New Zealand pasture pest, Costelytra giveni (Coleoptera: Scarabaeidae). Previous genomic profiling has shown that S. entomophila isolates appear to have conserved genomes and, where present, conserved plasmids. In the absence of C. giveni larvae, S. entomophila prevalence reduces in the soil over time, suggesting that S. entomophila has formed a host-specific relationship with C. giveni. To help define potential genetic mechanisms driving retention of the chronic disease of S. entomophila, the genome of the isolate 626 was sequenced, enabling the identification of unique chromosomal properties, and defining the gain/loss of accessory virulence factors relevant to pathogenicity to C. giveni larvae. RESULTS We report the complete sequence of S. entomophila isolate 626, a causal agent of amber disease in C. giveni larvae. The genome of S. entomophila 626 is 5,046,461 bp, with 59.1% G + C content and encoding 4,695 predicted CDS. Comparative analysis with five previously sequenced Serratia species, S. proteamaculans 336X, S. marcescens Db11, S. nematodiphila DH-S01, S. grimesii BXF1, and S. ficaria NBRC 102596, revealed a core of 1,165 genes shared. Further comparisons between S. entomophila 626 and S. proteamaculans 336X revealed fewer predicted phage-like regions and genomic islands in 626, suggesting less horizontally acquired genetic material. Genomic analyses revealed the presence of a four-gene itaconate operon, sharing a similar gene order as the Yersinia pestis ripABC complex. Assessment of a constructed 626::RipC mutant revealed that the operon confer a possible metabolic advantage to S. entomophila in the initial stages of C. giveni infection. CONCLUSIONS Evidence is presented where, relative to S. proteamaculans 336X, S. entomophila 626 encodes fewer genomic islands and phages, alluding to limited horizontal gene transfer in S. entomophila. Bioassay assessments of a S. entomophila-mutant with a targeted mutation of the itaconate degradation region unique to this species, found the mutant to have a reduced capacity to replicate post challenge of the C. giveni larval host, implicating the itaconate operon in establishment within the host.
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Affiliation(s)
- Amy L Vaughan
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand. .,AgResearch, Resilient Agriculture, Lincoln Research Centre, Christchurch, New Zealand.
| | - Eric Altermann
- AgResearch, Consumer Interface, Hopkirk Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Travis R Glare
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand
| | - Mark R H Hurst
- Bio-Protection Research Centre, Lincoln University, Lincoln, Christchurch, New Zealand.,AgResearch, Resilient Agriculture, Lincoln Research Centre, Christchurch, New Zealand
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13
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Coley WC, Akhavi A, Sandu C, Pena PA, Lee I, Ozkan M, Ozkan CS. Copper-carbon hybrid nanoparticles as antimicrobial additives. MRS COMMUNICATIONS 2022; 12:1197-1203. [PMID: 36284763 PMCID: PMC9584249 DOI: 10.1557/s43579-022-00294-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Millions of cases of hospital-acquired infections occur every year involving difficult to treat bacterial and fungal agents. In an effort to improve patient outcomes and provide better infection control, antimicrobial coatings are ideal to apply in clinical settings in addition to aseptic practices. Most efforts involving effective antimicrobial surface technologies are limited by toxicity of exposure due to the diffusion. Therefore, surface-immobilized antimicrobial agents are an ideal solution to infection control. Presented herein is a method of producing carbon-coated copper/copper oxide nanoparticles. Our findings demonstrate the potential for these particles to serve as antimicrobial additives. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1557/s43579-022-00294-2.
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Affiliation(s)
- William C. Coley
- Materials Science and Engineering Program, University of California, Riverside, CA 92521 USA
| | - Amirali Akhavi
- Materials Science and Engineering Program, University of California, Riverside, CA 92521 USA
| | - Cristina Sandu
- Materials Science and Engineering Program, University of California, Riverside, CA 92521 USA
| | - Pedro A. Pena
- Department of Chemistry, University of California, Riverside, CA 92521 USA
| | - Ilkeun Lee
- Department of Chemistry, University of California, Riverside, CA 92521 USA
| | - Mihrimah Ozkan
- Department of Chemistry, University of California, Riverside, CA 92521 USA
- Department of Electrical and Computer Engineering, University of California, Riverside, CA 92521 USA
| | - Cengiz S. Ozkan
- Department of Chemistry, University of California, Riverside, CA 92521 USA
- Department of Mechanical Engineering, University of California, Riverside, CA 92521 USA
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14
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Bottura B, Rooney LM, Hoskisson PA, McConnell G. Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness. Biofilm 2022; 4:100084. [PMID: 36254115 PMCID: PMC9568850 DOI: 10.1016/j.bioflm.2022.100084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 02/02/2023] Open
Abstract
Nutrient-transporting channels have been recently discovered in mature Escherichia coli biofilms, however the relationship between intra-colony channel structure and the surrounding environmental conditions is poorly understood. Using a combination of fluorescence mesoscopy and a purpose-designed open-source quantitative image analysis pipeline, we show that growth substrate composition and nutrient availability have a profound effect on the morphology of intra-colony channels in mature E. coli biofilms. Under all nutrient conditions, intra-colony channel width was observed to increase non-linearly with radial distance from the centre of the biofilm. Notably, the channels were around 25% wider at the centre of carbon-limited biofilms compared to nitrogen-limited biofilms. Channel density also differed in colonies grown on rich and minimal media, with the former creating a network of tightly packed channels and the latter leading to well-separated, wider channels with defined edges. Our approach paves the way for measurement of internal patterns in a wide range of biofilms, offering the potential for new insights into infection and pathogenicity.
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Affiliation(s)
- Beatrice Bottura
- Department of Physics, SUPA, University of Strathclyde, G4 0NG, Glasgow, UK,Corresponding author.
| | - Liam M. Rooney
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, G4 0RE, Glasgow, UK
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, G4 0RE, Glasgow, UK
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, G4 0NG, Glasgow, UK
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15
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Specht DA, Cortes LB, Lambert G. Overcoming Leak Sensitivity in CRISPRi Circuits Using Antisense RNA Sequestration and Regulatory Feedback. ACS Synth Biol 2022; 11:2927-2937. [PMID: 36017994 PMCID: PMC9486968 DOI: 10.1021/acssynbio.2c00155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 01/24/2023]
Abstract
The controlled binding of the catalytically dead CRISPR nuclease (dCas) to DNA can be used to create complex, programmable transcriptional genetic circuits, a fundamental goal of synthetic biology. This approach, called CRISPR interference (CRISPRi), is advantageous over existing methods because the programmable nature of CRISPR proteins in principle enables the simultaneous regulation of many different targets without crosstalk. However, the performance of dCas-based genetic circuits is limited by both the sensitivity to leaky repression within CRISPRi logic gates and retroactive effects due to a shared pool of dCas proteins. By utilizing antisense RNAs (asRNAs) to sequester gRNA transcripts as well as CRISPRi feedback to self-regulate asRNA production, we demonstrate a mechanism that suppresses unwanted repression by CRISPRi and improves logical gene circuit function in Escherichia coli. This improvement is particularly pronounced during stationary expression when CRISPRi circuits do not achieve the expected regulatory dynamics. Furthermore, the use of dual CRISPRi/asRNA inverters restores the logical performance of layered circuits such as a double inverter. By studying circuit induction at the single-cell level in microfluidic channels, we provide insight into the dynamics of antisense sequestration of gRNA and regulatory feedback on dCas-based repression and derepression. These results demonstrate how CRISPRi inverters can be improved for use in more complex genetic circuitry without sacrificing the programmability and orthogonality of dCas proteins.
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Affiliation(s)
- David A. Specht
- Applied Physics, Cornell University, Ithaca, New York 14853, United States
| | - Louis B. Cortes
- Applied Physics, Cornell University, Ithaca, New York 14853, United States
| | - Guillaume Lambert
- Applied Physics, Cornell University, Ithaca, New York 14853, United States
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16
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Khedr M, Khalil KMA, Kabary HA, Hamed AA, Badawy MSEM, Abu-Elghait M. Molecular docking and nucleotide sequencing of successive expressed recombinant fungal peroxidase gene in E.coli. J Genet Eng Biotechnol 2022; 20:94. [PMID: 35776246 PMCID: PMC9249955 DOI: 10.1186/s43141-022-00377-6] [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] [Received: 03/12/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022]
Abstract
Background Fungal peroxidases are oxidoreductases that utilize hydrogen peroxide to catalyze lignin biodegradation. Results PER-K (peroxidase synthesis codon gene) was transformed from Aspergillus niger strain AN512 deposited in the National Center for Biotechnology Information with the accession number OK323140 to Escherichia coli strain (BL21-T7 with YEp356R recombinant plasmid) via calcium chloride heat-shock method. The impact of four parameters (CaCl2 concentrations, centrifugation time, shaking speed, growth intensity) on the efficacy of the transformation process was evaluated. Furthermore, peroxidase production after optimization was assessed both qualitatively and quantitatively, as well as SDS-PAGE analysis. The optimum conditions for a successful transformation process were as follows: CaCl2 concentrations (50 mM), centrifugation time (20 min), shaking speed (200 rpm), and growth optical density (0.45). PCR and gel electrophoresis detect DNA bands with lengths 175, 179, and 211 bps corresponding to UA3, AmpR, and PER-K genes respectively besides partially sequencing the PER-K gene. Pyrogallol/hydrogen peroxide assay confirmed peroxidase production, and the activity of the enzyme was determined to be 3924 U/L. SDS-PAGE analysis also confirms peroxidase production illustrated by the appearance of a single peroxidase protein band after staining with Coomassie blue R-250. Conclusion A successful peroxidase-gene (PER-K) transformation from fungi to bacteria was performed correctly. The enzyme activity was screened, and partial sequencing of PER-K gene was analyzed successively. The protein 3D structure was generated via in silico homology modeling, and determination of binding sites and biological annotations of the constructed protein were carried out via COACH and COFACTOR based on the I-TASSER structure prediction. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00377-6.
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Affiliation(s)
- Mohamed Khedr
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt
| | - Kamal M A Khalil
- Genetic Engineering and Biotechnology Division, Genetics and Cytology Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Hoda A Kabary
- Agricultural Microbiology Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Ahmed A Hamed
- Microbial Chemistry Department, National Research Centre, 33 El-Buhouth Street, Dokki, Cairo, 12622, Egypt
| | - Mona Shaban E M Badawy
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Mohammed Abu-Elghait
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, 11884 Nasr City, Cairo, Egypt.
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17
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Bhadra S, Paik I, Torres JA, Fadanka S, Gandini C, Akligoh H, Molloy J, Ellington AD. Preparation and Use of Cellular Reagents: A Low-resource Molecular Biology Reagent Platform. Curr Protoc 2022; 2:e387. [PMID: 35263038 PMCID: PMC9094432 DOI: 10.1002/cpz1.387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein reagents are indispensable for most molecular and synthetic biology procedures. Most conventional protocols rely on highly purified protein reagents that require considerable expertise, time, and infrastructure to produce. In consequence, most proteins are acquired from commercial sources, reagent expense is often high, and accessibility may be hampered by shipping delays, customs barriers, geopolitical constraints, and the need for a constant cold chain. Such limitations to the widespread availability of protein reagents, in turn, limit the expansion and adoption of molecular biology methods in research, education, and technology development and application. Here, we describe protocols for producing a low-resource and locally sustainable reagent delivery system, termed "cellular reagents," in which bacteria engineered to overexpress proteins of interest are dried and can then be used directly as reagent packets in numerous molecular biology reactions, without the need for protein purification or a constant cold chain. As an example of their application, we describe the execution of polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) using cellular reagents, detailing how to replace pure protein reagents with optimal amounts of rehydrated cellular reagents. We additionally describe a do-it-yourself fluorescence visualization device for using these cellular reagents in common molecular biology applications. The methods presented in this article can be used for low-cost, on-site production of commonly used molecular biology reagents (including DNA and RNA polymerases, reverse transcriptases, and ligases) with minimal instrumentation and expertise, and without the need for protein purification. Consequently, these methods should generally make molecular biology reagents more affordable and accessible. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of cellular reagents Alternate Protocol 1: Preparation of lyophilized cellular reagents Alternate Protocol 2: Evaluation of bacterial culture growth via comparison to McFarland turbidity standards Support Protocol 1: SDS-PAGE for protein expression analysis of cellular reagents Basic Protocol 2: Using Taq DNA polymerase cellular reagents for PCR Basic Protocol 3: Using Br512 DNA polymerase cellular reagents for loop-mediated isothermal amplification (LAMP) Support Protocol 2: Building a fluorescence visualization device.
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Affiliation(s)
- Sanchita Bhadra
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America,Corresponding authors: ,
| | - Inyup Paik
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jose-Angel Torres
- Freshman Research Initiative, DIY Diagnostics Stream, The University of Texas at Austin, Austin, Texas, United States of America
| | | | - Chiara Gandini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Harry Akligoh
- Hive Biolab, Hse 49, SE 29056 Drive, 2nd Turn Behind Mizpah School, Kentinkrono, Kumasi, Ghana
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas, United States of America,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, United States of America,Corresponding authors: ,
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18
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Pseudomonas spp. Mediate defense response in sugarcane through differential exudation of root phenolics. Saudi J Biol Sci 2021; 28:7528-7538. [PMID: 34867057 PMCID: PMC8626327 DOI: 10.1016/j.sjbs.2021.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/11/2021] [Accepted: 09/12/2021] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas spp., a ubiquitous biocontrol agent, protects the plants from phytopathogens by suppressing them directly by reinforcing the plant’s intrinsic defense mechanism. Root exudated phenolics play an important role in establishing the rhizobacteria population and cross the host boundaries in beneficial plant–microbe interaction. In this study, Pseudomonas spp. HU-8 & HU-9 antagonized the sugarcane red rot pathogen (C. falcatum) and showed a positive chemotactic response against different concentrations (10–30 µM) of synthetic phenolic acids like p-coumaric, vanillic, and 3,4 di-hydroxybenzoic acid. In a pot experiment, they effectively colonized the sugarcane rhizosphere and mediated defense response in sugarcane plants challenged with red rot pathogen C. falcatum by regulating the exudation of root phenolics under hydroponic conditions. They significantly induced the activity of the antioxidant enzymes CAT (1.24–1.64 fold), PO (0.78–1.61 fold), PAL (0.77–0.97 fold), and PPO (3.67–3.73 fold) over untreated plants in sugarcane. They also induced the total phenolic contents (TPC) in sugarcane in the presence (6.56–10.29 mg/g GAE) and absence (2.89–4.16 mg/g GAE) of the pathogen quantified through the Folin-Ciocalteu (FC) method. However, their effect was lower than that of the pathogen (4.34–8 mg/g GAE). The Pseudomonas spp. significantly colonized the sugarcane rhizosphere by maintaining a cell population of (1.0E + 07–1.3E + 08 CFU/mL). A significant positive Pearson’s correlation was observed between the root exudated total phenolic contents, antioxidant enzymatic activities, and rhizospheric population of inoculated bacteria. The 16S rRNA and rpoD gene analysis showed sequence conservation (C: 0.707), average number of nucleotide differences (k: 199.816), nucleotide diversity, (Pi): 0.09819), average number of informative nucleotide sites per site (Psi: 0.01275), GC content (0.57), and polymorphic sites (n = 656). These diverse Pseudomonas spp. could be an ideal bio-inoculants for a broad range of hosts especially graminaceous crops.
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19
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Novoskoltseva OA, Panova IG, Loiko NG, Nikolaev YA, Litmanovich EA, Yaroslavov AA. Polyelectrolytes and Polycomplexes for Stabilizing Sandy Grounds. POLYMER SCIENCE SERIES B 2021. [DOI: 10.1134/s1560090421050092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Infrared-spectroscopic, dynamic near-field microscopy of living cells and nanoparticles in water. Sci Rep 2021; 11:21860. [PMID: 34750511 PMCID: PMC8576021 DOI: 10.1038/s41598-021-01425-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
Infrared fingerprint spectra can reveal the chemical nature of materials down to 20-nm detail, far below the diffraction limit, when probed by scattering-type scanning near-field optical microscopy (s-SNOM). But this was impossible with living cells or aqueous processes as in corrosion, due to water-related absorption and tip contamination. Here, we demonstrate infrared s-SNOM of water-suspended objects by probing them through a 10-nm thick SiN membrane. This separator stretches freely over up to 250 µm, providing an upper, stable surface to the scanning tip, while its lower surface is in contact with the liquid and localises adhering objects. We present its proof-of-principle applicability in biology by observing simply drop-casted, living E. coli in nutrient medium, as well as living A549 cancer cells, as they divide, move and develop rich sub-cellular morphology and adhesion patterns, at 150 nm resolution. Their infrared spectra reveal the local abundances of water, proteins, and lipids within a depth of ca. 100 nm below the SiN membrane, as we verify by analysing well-defined, suspended polymer spheres and through model calculations. SiN-membrane based s-SNOM thus establishes a novel tool of live cell nano-imaging that returns structure, dynamics and chemical composition. This method should benefit the nanoscale analysis of any aqueous system, from physics to medicine.
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21
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Novoskoltseva OA, Loiko NG, Nikolaev YA, Lisin AO, Panova IG, Yaroslavov AA. Interpolyelectrolyte complexes based on hydrolyzed polyacrylonitrile for anti‐erosion stabilization of soils and ground. POLYM INT 2021. [DOI: 10.1002/pi.6289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Natalia G Loiko
- Federal State Institution, Federal Research Centre ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences Moscow Russia
| | - Yury A Nikolaev
- Federal State Institution, Federal Research Centre ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences Moscow Russia
| | - Andrey O Lisin
- Lomonosov Moscow State University Faculty of Chemistry Moscow Russia
| | - Irina G Panova
- Lomonosov Moscow State University Faculty of Chemistry Moscow Russia
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22
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Abstract
In this paper, the artificial bee colony (ABC) algorithm is hybridized with the genetic algorithm (GA) for a model parameter identification problem. When dealing with real-world and large-scale problems, it becomes evident that concentrating on a sole metaheuristic algorithm is somewhat restrictive. A skilled combination between metaheuristics or other optimization techniques, a so-called hybrid metaheuristic, can provide more efficient behavior and greater flexibility. Hybrid metaheuristics combine the advantages of one algorithm with the strengths of another. ABC, based on the foraging behavior of honey bees, and GA, based on the mechanics of nature selection, are among the most efficient biologically inspired population-based algorithms. The performance of the proposed ABC-GA hybrid algorithm is examined, including classic benchmark test functions. To demonstrate the effectiveness of ABC-GA for a real-world problem, parameter identification of an Escherichia coli MC4110 fed-batch cultivation process model is considered. The computational results of the designed algorithm are compared to the results of different hybridized biologically inspired techniques (ant colony optimization (ACO) and firefly algorithm (FA))—hybrid algorithms as ACO-GA, GA-ACO and ACO-FA. The algorithms are applied to the same problems—a set of benchmark test functions and the real nonlinear optimization problem. Taking into account the overall searchability and computational efficiency, the results clearly show that the proposed ABC–GA algorithm outperforms the considered hybrid algorithms.
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23
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Bower OJ, McCarthy A, Lea RA, Alanis-Lobato G, Zohren J, Gerri C, Turner JMA, Niakan KK. Generating CRISPR-Cas9-Mediated Null Mutations and Screening Targeting Efficiency in Human Pluripotent Stem Cells. Curr Protoc 2021; 1:e232. [PMID: 34432381 DOI: 10.1002/cpz1.232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
CRISPR-Cas9 mutagenesis facilitates the investigation of gene function in a number of developmental and cellular contexts. Human pluripotent stem cells (hPSCs), either embryonic or induced, are a tractable cellular model to investigate molecular mechanisms involved in early human development and cell fate decisions. hPSCs also have broad potential in regenerative medicine to model, investigate, and ameliorate diseases. Here, we provide an optimized protocol for efficient CRISPR-Cas9 genome editing of hPSCs to investigate the functional role of genes by engineering null mutations. We emphasize the importance of screening single guide RNAs (sgRNAs) to identify those with high targeting efficiency for generation of clonally derived null mutant hPSC lines. We provide important considerations for targeting genes that may have a role in hPSC maintenance. We also present methods to evaluate the on-target mutation spectrum and unintended karyotypic changes. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Selecting and ligating sgRNAs into expression plasmids Basic Protocol 2: Validation of sgRNA via in vitro transcription and cleavage assay Basic Protocol 3: Nucleofection of primed human embryonic stem cells Basic Protocol 4: MiSeq analysis of indel mutations Basic Protocol 5: Single cell cloning of targeted hPSCs Basic Protocol 6: Karyotyping of targeted hPSCs.
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Affiliation(s)
- Oliver J Bower
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Rebecca A Lea
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Gregorio Alanis-Lobato
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Jasmin Zohren
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Claudia Gerri
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
- The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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24
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Song J, Tóth K, Montes-Luz B, Stacey G. Soybean Hairy Root Transformation: A Rapid and Highly Efficient Method. Curr Protoc 2021; 1:e195. [PMID: 34288607 DOI: 10.1002/cpz1.195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
New genetic engineering techniques have advanced the field of plant molecular biology, and Agrobacterium-mediated transformation has enabled the discovery of numerous molecular and genetic functions. It has been widely used in many plants, including the economically important crop, soybean. Large-scale genetic analyses are needed to comprehend the molecular mechanisms that underlie the agronomic traits of soybean, and the generation of stable transgenic plants involves a lengthy and laborious process. Agrobacterium rhizogenes-mediated hairy root transformation is a quick and efficient method for investigations of root-specific processes and interactions. Generation of composite plants with transgenic roots and wild-type shoots allows for the study of the genetic mechanisms involved in root biology, such as the Bradyrhizobium-soybean interaction. Here, we provide an updated protocol for generating hairy soybean roots in as little as 18 days in a cost- and space-effective manner and demonstrate possible uses of composite plants with soybean nodulation assays and gene expression analysis as examples. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Soybean hairy root transformation Basic Protocol 2: Soybean nodulation assay Alternate Protocol: Soybean nodulation assay in germination pouches Support Protocol: Bradyrhizobium japonicum culture preparation for inoculation Basic Protocol 3: Histochemical GUS staining for promoter analysis.
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Affiliation(s)
- Jaehyo Song
- Division of Plant Sciences, University of Missouri, Columbia, Missouri
| | - Katalin Tóth
- Division of Plant Sciences, University of Missouri, Columbia, Missouri
- Ecology and Genetics Research Unit, Faculty of Science, University of Oulu, Oulu, Finland
| | - Bruna Montes-Luz
- Division of Plant Sciences, University of Missouri, Columbia, Missouri
| | - Gary Stacey
- Division of Plant Sciences, University of Missouri, Columbia, Missouri
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25
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Liu Y, Westover KD. Rapid assessment of DCLK1 inhibitors using a peptide substrate mobility shift assay. STAR Protoc 2021; 2:100587. [PMID: 34159321 PMCID: PMC8203847 DOI: 10.1016/j.xpro.2021.100587] [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] [Indexed: 11/28/2022] Open
Abstract
Peptide mobility shift assays provide a sensitive measure of kinase enzymatic activity and can be used to evaluate kinase inhibitors. Herein, we describe a protocol adapted for rapid assessment of doublecortin-like kinase inhibitors. Advantages include rapid iterations of therapeutic compound assessment and the ability to characterize kinase mutations, such as drug-resistant mutants for biological rescue experiments, on kinase activity. For complete details on the use and execution of this protocol, please refer to Liu et al. (2020). A peptide substrate mobility shift assay (MSA) measures DCLK1 kinase activity The MSA platform can generate enzyme kinetics data The MSA enables sensitive rank ordering of DCLK1 kinase inhibitors The assay is compatible with a 384-well format
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Affiliation(s)
- Yan Liu
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Kenneth D Westover
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
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26
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Sitter TL, Vaughan AL, Schoof M, Jackson SA, Glare TR, Cox MP, Fineran PC, Gardner PP, Hurst MRH. Evolution of virulence in a novel family of transmissible mega-plasmids. Environ Microbiol 2021; 23:5289-5304. [PMID: 33989447 DOI: 10.1111/1462-2920.15595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/27/2022]
Abstract
Some Serratia entomophila isolates have been successfully exploited in biopesticides due to their ability to cause amber disease in larvae of the Aotearoa (New Zealand) endemic pasture pest, Costelytra giveni. Anti-feeding prophage and ABC toxin complex virulence determinants are encoded by a 153-kb single-copy conjugative plasmid (pADAP; amber disease-associated plasmid). Despite growing understanding of the S. entomophila pADAP model plasmid, little is known about the wider plasmid family. Here, we sequence and analyse mega-plasmids from 50 Serratia isolates that induce variable disease phenotypes in the C. giveni insect host. Mega-plasmids are highly conserved within S. entomophila, but show considerable divergence in Serratia proteamaculans with other variants in S. liquefaciens and S. marcescens, likely reflecting niche adaption. In this study to reconstruct ancestral relationships for a complex mega-plasmid system, strong co-evolution between Serratia species and their plasmids were found. We identify 12 distinct mega-plasmid genotypes, all sharing a conserved gene backbone, but encoding highly variable accessory regions including virulence factors, secondary metabolite biosynthesis, Nitrogen fixation genes and toxin-antitoxin systems. We show that the variable pathogenicity of Serratia isolates is largely caused by presence/absence of virulence clusters on the mega-plasmids, but notably, is augmented by external chromosomally encoded factors.
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Affiliation(s)
- Thomas L Sitter
- Forage Science, AgResearch, Lincoln Research Centre, Christchurch, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Amy L Vaughan
- Forage Science, AgResearch, Lincoln Research Centre, Christchurch, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Marion Schoof
- Forage Science, AgResearch, Lincoln Research Centre, Christchurch, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Murray P Cox
- Bio-Protection Research Centre, Lincoln, New Zealand.,Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Peter C Fineran
- Bio-Protection Research Centre, Lincoln, New Zealand.,Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Paul P Gardner
- Bio-Protection Research Centre, Lincoln, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Mark R H Hurst
- Forage Science, AgResearch, Lincoln Research Centre, Christchurch, New Zealand.,Bio-Protection Research Centre, Lincoln, New Zealand
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27
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Sari‐Ak D, Bufton J, Gupta K, Garzoni F, Fitzgerald D, Schaffitzel C, Berger I. VLP-factory™ and ADDomer © : Self-assembling Virus-Like Particle (VLP) Technologies for Multiple Protein and Peptide Epitope Display. Curr Protoc 2021; 1:e55. [PMID: 33729713 PMCID: PMC9733710 DOI: 10.1002/cpz1.55] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Virus-like particles (VLPs) play a prominent role in vaccination as safe and highly versatile alternatives to attenuated or inactivated viruses or subunit vaccines. We present here two innovations, VLP-factory™ and ADDomer© , for creating VLPs displaying entire proteins or peptide epitopes as antigens, respectively, to enable efficient vaccination. For producing these VLPs, we use MultiBac, a baculovirus expression vector system (BEVS) that we developed for producing complex protein biologics in insect cells transfected with an engineered baculovirus. VLPs are protein assemblies that share features with viruses but are devoid of genetic material, and thus considered safe. VLP-factory™ represents a customized MultiBac baculovirus tailored to produce enveloped VLPs based on the M1 capsid protein of influenza virus. We apply VLP-factory™ to create an array of influenza-derived VLPs presenting functional mutant influenza hemagglutinin (HA) glycoprotein variants. Moreover, we describe MultiBac-based production of ADDomer© , a synthetic self-assembling adenovirus-derived protein-based VLP platform designed to display multiple copies of pathogenic epitopes at the same time on one particle for highly efficient vaccination. © 2021 The Authors. Basic Protocol 1: VLP-factory™ baculoviral genome generation Basic Protocol 2: Influenza VLP array generation using VLP-factory™ Basic Protocol 3: Influenza VLP purification Basic Protocol 4: ADDomer© BioBrick design, expression, and purification Basic Protocol 5: ADDomer© candidate vaccines against infectious diseases.
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Affiliation(s)
- Duygu Sari‐Ak
- Department of Medical Biology, School of MedicineUniversity of Health SciencesIstanbulTurkey
| | - Joshua Bufton
- Bristol Synthetic Biology Centre BrisSynBioUniversity of BristolBristolUnited Kingdom,School of Biochemistry, Biomedical SciencesUniversity of BristolBristolUnited Kingdom
| | - Kapil Gupta
- Bristol Synthetic Biology Centre BrisSynBioUniversity of BristolBristolUnited Kingdom,School of Biochemistry, Biomedical SciencesUniversity of BristolBristolUnited Kingdom
| | - Frederic Garzoni
- Imophoron Ltd, St. Philips CentralSt. PhilipsBristolUnited Kingdom
| | | | - Christiane Schaffitzel
- Bristol Synthetic Biology Centre BrisSynBioUniversity of BristolBristolUnited Kingdom,School of Biochemistry, Biomedical SciencesUniversity of BristolBristolUnited Kingdom
| | - Imre Berger
- Bristol Synthetic Biology Centre BrisSynBioUniversity of BristolBristolUnited Kingdom,School of Biochemistry, Biomedical SciencesUniversity of BristolBristolUnited Kingdom,School of ChemistryUniversity of BristolBristolUnited Kingdom,Max Planck Bristol Centre for Minimal BiologyUniversity of BristolBristolUnited Kingdom
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28
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Marillonnet S, Grützner R. Synthetic DNA Assembly Using Golden Gate Cloning and the Hierarchical Modular Cloning Pipeline. ACTA ACUST UNITED AC 2021; 130:e115. [PMID: 32159931 DOI: 10.1002/cpmb.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Methods that enable the construction of recombinant DNA molecules are essential tools for biological research and biotechnology. Golden Gate cloning is used for assembly of multiple DNA fragments in a defined linear order in a recipient vector using a one-pot assembly procedure. Golden Gate cloning is based on the use of a type IIS restriction enzyme for digestion of the DNA fragments and vector. Because restriction sites for the type IIS enzyme used for assembly must be present at the ends of the DNA fragments and vector but absent from all internal sequences, special care must be taken to prepare DNA fragments and the recipient vector with a structure suitable for assembly by Golden Gate cloning. In this article, protocols are presented for preparation of DNA fragments, modules, and vectors suitable for Golden Gate assembly cloning. Additional protocols are presented for assembly of defined parts in a transcription unit, as well as the stitching together of multiple transcription units into multigene constructs by the modular cloning (MoClo) pipeline. © 2020 The Authors. Basic Protocol 1: Performing a typical Golden Gate cloning reaction Basic Protocol 2: Accommodating a vector to Golden Gate cloning Basic Protocol 3: Accommodating an insert to Golden Gate cloning Basic Protocol 4: Generating small standardized parts compatible with hierarchical modular cloning (MoClo) using level 0 vectors Alternate Protocol: Generating large standardized parts compatible with hierarchical modular cloning (MoClo) using level -1 vectors Basic Protocol 5: Assembling transcription units and multigene constructs using level 1, M, and P MoClo vectors.
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Affiliation(s)
- Sylvestre Marillonnet
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Halle, Germany
| | - Ramona Grützner
- Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, Halle, Germany
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29
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A Phosphonate Natural Product Made by Pantoea ananatis is Necessary and Sufficient for the Hallmark Lesions of Onion Center Rot. mBio 2021; 12:mBio.03402-20. [PMID: 33531390 PMCID: PMC7858074 DOI: 10.1128/mbio.03402-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pantoea ananatis is the primary cause of onion center rot. Genetic data suggest that a phosphonic acid natural product is required for pathogenesis; however, the nature of the molecule is unknown. Here, we show that P. ananatis produces at least three phosphonates, two of which were purified and structurally characterized. The first, designated pantaphos, was shown to be 2-(hydroxy[phosphono]methyl)maleate; the second, a probable biosynthetic precursor, was shown to be 2-(phosphonomethyl)maleate. Purified pantaphos is both necessary and sufficient for the hallmark lesions of onion center rot. Moreover, when tested against mustard seedlings, the phytotoxic activity of pantaphos was comparable to the widely used herbicides glyphosate and phosphinothricin. Pantaphos was also active against a variety of human cell lines but was significantly more toxic to glioblastoma cells. Pantaphos showed little activity when tested against a variety of bacteria and fungi.IMPORTANCE Pantoea ananatis is a significant plant pathogen that targets a number of important crops, a problem that is compounded by the absence of effective treatments to prevent its spread. Our identification of pantaphos as the key virulence factor in onion center rot suggests a variety of approaches that could be employed to address this significant plant disease. Moreover, the general phytotoxicity of the molecule suggests that it could be developed into an effective herbicide to counter the alarming rise in herbicide-resistant weeds.
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30
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Tuttle AR, Trahan ND, Son MS. Growth and Maintenance of Escherichia coli Laboratory Strains. Curr Protoc 2021; 1:e20. [PMID: 33484484 DOI: 10.1002/cpz1.20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Escherichia coli is a Gram-negative bacterium, commonly used in both teaching and research laboratories. This article includes protocols for the growth and maintenance of E. coli in any teaching- or research-associated laboratory. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Growth of E. coli from frozen stocks Basic Protocol 2: Growth of E. coli in liquid media Basic Protocol 3: Enumeration of E. coli on solid media Basic Protocol 4: Storage of E. coli frozen stocks in glycerol Basic Protocol 5: Storage of E. coli in agar stabs Basic Protocol 6: Growth curve of E. coli liquid culture.
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Affiliation(s)
| | | | - Mike S Son
- Plymouth State University, Plymouth, New Hampshire
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31
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Vaitkus S, Simoes-Torigoe R, Wong N, Morris K, Spada FE, Alagiri M, Talke FE. A comparative study of experimental urinary catheters containing silver and zinc for biofilm inhibition. J Biomater Appl 2021; 35:1071-1081. [PMID: 33478312 DOI: 10.1177/0885328221989553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Both commercial and experimental antibacterial urinary catheters were investigated for their efficacy in preventing planktonic growth and biofilm formation of Escherichia Coli bacteria in a synthetic urine solution. Experimental antibacterial catheters having thin (<500 µm) dispersions of Ag, Ag/Ag2O, or Zn/Ag2O in polydimethylsiloxane (PDMS) binder all exhibited significant antimicrobial activity, outperforming traditional commercial antibacterial catheters. All experimental catheters prevented planktonic growth of bacteria and did not exhibit biofilm formation during a six-day test period using a colony forming unit (CFU) measurement method. On the other hand, the best performing commercial catheters demonstrated efficacy for only 3 days in planktonic growth tests and formed multiple bacterial colonies in CFU measurements. The Zn/Ag2O/PDMS experimental catheter was the only catheter observed to produce hydrogen peroxide, a reactive oxygen species known to inhibit biofilm formation; lack of detectable hydrogen peroxide production by the Ag2O/PDMS and Ag/Ag2O/PDMS experimental catheters suggests that bactericidal action most likely arises from release of silver ions present in the PDMS coatings.
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Affiliation(s)
- Simonas Vaitkus
- UCSD Center for Memory and Recording Research, La Jolla, CA, USA
| | | | - Nicholas Wong
- UCSD Center for Memory and Recording Research, La Jolla, CA, USA
| | - Karcher Morris
- UCSD Center for Memory and Recording Research, La Jolla, CA, USA
| | | | | | - Frank E Talke
- UCSD Center for Memory and Recording Research, La Jolla, CA, USA
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32
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Vasquez CA, Cowan QT, Komor AC. Base Editing in Human Cells to Produce Single-Nucleotide-Variant Clonal Cell Lines. ACTA ACUST UNITED AC 2020; 133:e129. [PMID: 33151638 DOI: 10.1002/cpmb.129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Base-editing technologies enable the introduction of point mutations at targeted genomic sites in mammalian cells, with higher efficiency and precision than traditional genome-editing methods that use DNA double-strand breaks, such as zinc finger nucleases (ZFNs), transcription-activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (CRISPR-Cas9) system. This allows the generation of single-nucleotide-variant isogenic cell lines (i.e., cell lines whose genomic sequences differ from each other only at a single, edited nucleotide) in a more time- and resource-effective manner. These single-nucleotide-variant clonal cell lines represent a powerful tool with which to assess the functional role of genetic variants in a native cellular context. Base editing can therefore facilitate genotype-to-phenotype studies in a controlled laboratory setting, with applications in both basic research and clinical applications. Here, we provide optimized protocols (including experimental design, methods, and analyses) to design base-editing constructs, transfect adherent cells, quantify base-editing efficiencies in bulk, and generate single-nucleotide-variant clonal cell lines. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Design and production of plasmids for base-editing experiments Basic Protocol 2: Transfection of adherent cells and harvesting of genomic DNA Basic Protocol 3: Genotyping of harvested cells using Sanger sequencing Alternate Protocol 1: Next-generation sequencing to quantify base editing Basic Protocol 4: Single-cell isolation of base-edited cells using FACS Alternate Protocol 2: Single-cell isolation of base-edited cells using dilution plating Basic Protocol 5: Clonal expansion to generate isogenic cell lines and genotyping of clones.
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Affiliation(s)
- Carlos A Vasquez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
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33
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ERKOC P. Sodium Borohydride and Essential Oils as Reducing Agents for the Chemically and Green Synthesis of Silver Nanoparticles: A Comparative Analysis. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2020. [DOI: 10.18596/jotcsa.737566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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34
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Rooney LM, Amos WB, Hoskisson PA, McConnell G. Intra-colony channels in E. coli function as a nutrient uptake system. THE ISME JOURNAL 2020; 14:2461-2473. [PMID: 32555430 PMCID: PMC7490401 DOI: 10.1038/s41396-020-0700-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
The ability of microorganisms to grow as aggregated assemblages has been known for many years, however their structure has remained largely unexplored across multiple spatial scales. The development of the Mesolens, an optical system which uniquely allows simultaneous imaging of individual bacteria over a 36 mm2 field of view, has enabled the study of mature Escherichia coli macro-colony biofilm architecture like never before. The Mesolens enabled the discovery of intra-colony channels on the order of 10 μm in diameter, that are integral to E. coli macro-colony biofilms and form as an emergent property of biofilm growth. These channels have a characteristic structure and re-form after total mechanical disaggregation of the colony. We demonstrate that the channels are able to transport particles and play a role in the acquisition of and distribution of nutrients through the biofilm. These channels potentially offer a new route for the delivery of dispersal agents for antimicrobial drugs to biofilms, ultimately lowering their impact on public health and industry.
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Affiliation(s)
- Liam M Rooney
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK.
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
| | - William B Amos
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
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35
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Sarrion-Perdigones A, Chang L, Gonzalez Y, Gallego-Flores T, Young DW, Venken KJT. Simultaneous Examination of Cellular Pathways using Multiplex Hextuple Luciferase Assaying. ACTA ACUST UNITED AC 2020; 131:e122. [PMID: 32539239 DOI: 10.1002/cpmb.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Multiplex experimentation that can assay multiple cellular signaling pathways in the same cells requires orthogonal genetically encoded reporters that report over large dynamic ranges. Luciferases are cost-effective, versatile candidates whose output signals can be sensitively detected in a multiplex fashion. Commonly used dual luciferase reporter assays detect one luciferase that is coupled to a single cellular pathway and a second that is coupled to a control pathway for normalization purposes. We have expanded this approach to multiplex hextuple luciferase assays that can report on five cellular signaling pathways and one control, each of which is encoded by a unique luciferase. Light emission by the six luciferases can be distinguished by the use of two distinct substrates, each specific for three luciferases, followed by spectral decomposition of the light emitted by each of the three luciferase enzymes with bandpass filters. Here, we present detailed protocols on how to perform multiplex hextuple luciferase assaying to monitor pathway fluxes through transcriptional response elements for five specific signaling pathways (i.e., c-Myc, NF-κβ, TGF-β, p53, and MAPK/JNK) using the constitutive CMV promoter as normalization control. Protocols are provided for preparing reporter vector plasmids for multiplex reporter assaying, performing cell culture and multiplex luciferase reporter vector plasmid transfection, executing multiplex luciferase assays, and analyzing and interpreting data obtained by a plate reader appropriately equipped to detect the different luminescences. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of vectors for multiplex hextuple luciferase assaying Basic Protocol 2: Cell culture work for multiplex hextuple luciferase assays Basic Protocol 3: Transfection of luciferase reporter plasmids followed by drug and recombinant protein treatments Basic Protocol 4: Performing the multiplex hextuple luciferase assay.
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Affiliation(s)
- Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Lyra Chang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Tatiana Gallego-Flores
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Current address: Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Damian W Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas.,McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, Texas
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36
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Sarrion-Perdigones A, Gonzalez Y, Venken KJT. Rapid and Efficient Synthetic Assembly of Multiplex Luciferase Reporter Plasmids for the Simultaneous Monitoring of Up to Six Cellular Signaling Pathways. ACTA ACUST UNITED AC 2020; 131:e121. [PMID: 32539183 DOI: 10.1002/cpmb.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High-throughput cell-based screening assays are valuable tools in the discovery of chemical probes and therapeutic agents. Such assays are designed to examine the effects of small compounds on targets, pathways, or phenotypes participating in normal and disease processes. While most cell-based assays measure single quantities, multiplexed assays seek to address these limitations by obtaining multiple simultaneous measurements. The signals from such measurements should be independently detectable and cover large dynamic ranges. Luciferases are good candidates for generation of such signals. They are genetically encoded, versatile, and cost-effective, and their output signals can be sensitively detected. We recently developed a multiplex luciferase assay that allows monitoring the activity of five experimental pathways against one control simultaneously. We used synthetic assembly cloning to assemble all six luciferase reporter units into a single vector over eight stitching rounds. Because all six reporters are on a single piece of DNA, a single vector ensures stoichiometric ratios of each transcriptional unit in each transfected cell, resulting in lower experimental variation. Our proof-of-concept multiplex hextuple luciferase assay was designed to simultaneously monitor the p53, TGF-β, NF-κβ, c-Myc, and MAPK/JNK signaling pathways. The same synthetic assembly cloning pipeline allows the stitching of numerous other cellular pathway luciferase reporters. Here we present an improved three-step synthetic assembly protocol to quickly and efficiently generate multiplex hextuple luciferase reporter plasmids for other signaling pathways of interest. This improved assembly protocol provides the opportunity to analyze any five desired pathways at once much more quickly. Protocols are provided on how to prepare DNA components and destination vector plasmids, design synthetic DNA, perform assembly cloning of new transcriptional reporter elements, implement multipartite synthetic assembly cloning of single-pathway luciferase reporters, and carry out one-step assembly of final multiplex hextuple luciferase vectors. We present protocols on how to perform multiplex hextuple luciferase in an accompanying Current Protocols in Molecular Biology article. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of DNA parts and destination vectors for synthetic assembly cloning Basic Protocol 2: DNA synthesis and assembly cloning of a typical transcriptional reporter element Alternate Protocol: DNA synthesis and assembly cloning of a challenging transcriptional reporter element Basic Protocol 3: Multipartite synthetic assembly cloning of individual pathway luciferase reporters Basic Protocol 4: One step assembly into final multiplex hextuple luciferase vectors Support Protocol: Generation of home-made chemocompetent E. coli DH10B-T1R cells.
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Affiliation(s)
- Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas.,McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, Texas
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37
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Neumayr C, Pagani M, Stark A, Arnold CD. STARR-seq and UMI-STARR-seq: Assessing Enhancer Activities for Genome-Wide-, High-, and Low-Complexity Candidate Libraries. ACTA ACUST UNITED AC 2020; 128:e105. [PMID: 31503413 PMCID: PMC9286403 DOI: 10.1002/cpmb.105] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The identification of transcriptional enhancers and the quantitative assessment of enhancer activities is essential to understanding how regulatory information for gene expression is encoded in animal and human genomes. Further, it is key to understanding how sequence variants affect enhancer function. STARR‐seq enables the direct and quantitative assessment of enhancer activity for millions of candidate sequences of arbitrary length and origin in parallel, allowing the screening of entire genomes and the establishment of genome‐wide enhancer activity maps. In STARR‐seq, the candidate sequences are cloned downstream of the core promoter into a reporter gene's transcription unit (i.e., the 3′ UTR). Candidates that function as active enhancers lead to the transcription of reporter mRNAs that harbor the candidates’ sequences. This direct coupling of enhancer sequence and enhancer activity in cis enables the straightforward and efficient cloning of complex candidate libraries and the assessment of enhancer activities of millions of candidates in parallel by quantifying the reporter mRNAs by deep sequencing. This article describes how to create focused and genome‐wide human STARR‐seq libraries and how to perform STARR‐seq screens in mammalian cells, and also describes a novel STARR‐seq variant (UMI‐STARR‐seq) that allows the accurate counting of reporter mRNAs for STARR‐seq libraries of low complexity. © 2019 The Authors. Basic Protocol 1: STARR‐seq plasmid library cloning Basic Protocol 2: Mammalian STARR‐seq screening protocol Alternate Protocol: UMI‐STARR‐seq screening protocol—unique molecular identifier integration Support Protocol: Transfection of human cells using the MaxCyte STX scalable transfection system
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Affiliation(s)
- Christoph Neumayr
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.,Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Cosmas D Arnold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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Moody LV, Miyamoto Y, Ang J, Richter PJ, Eckmann L. Evaluation of Peroxides and Chlorine Oxides as Disinfectants for Chemical Sterilization of Gnotobiotic Rodent Isolators. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2019; 58:558-568. [PMID: 31319899 PMCID: PMC6774453 DOI: 10.30802/aalas-jaalas-18-000130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/17/2018] [Accepted: 02/14/2019] [Indexed: 12/22/2022]
Abstract
Gnotobiotic animal research has expanded markedly over the past decade. Although germ-free animals were first described more than 100 y ago, little evidence-based guidance is available on best operational procedures. A key aspect of gnotobiotic technology is the sterilization of animal enclosures, most commonly flexible vinyl film isolators. The objective of this study was to determine the most effective methods for chemical sterilization of gnotobiotic isolators and associated equipment. As test microbes, we used bacteria from 4 different accidental isolator contaminations that occurred in a gnotobiotic core facility. Identification by 16S ribotyping revealed facultative anaerobic firmicutes, including several Paenibacillus and Bacillus species, and obligate aerobic actinobacteria, namely Micrococcus luteus, among the contaminants. We selected 6 products commonly used for disinfecting hospital rooms, kitchens, and veterinary facilities to represent chlorine-oxide- and peroxide-based disinfectants and tested the hypothesis that these 2 classes are equally effective. However, evaluation of bactericidal and sporicidal activity in liquid cultures revealed that chlorine oxide-based disinfectants were more effective than peroxide-based disinfectants. In both groups, various products effectively sterilized gnotobiotic isolators by fogging in field tests, although bactericidal concentrations were markedly higher than those in suspension cultures, and effectiveness was contact-time-dependent. In addition, in both groups, some disinfectants were excessively corrosive to ferrous metals and acrylic. These results demonstrate that no single disinfectant has all desirable properties and that the different characteristics of disinfectants must be balanced during their selection. However, chlorine oxide-based disinfectants were generally more effective and less corrosive than peroxide-based products.
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Affiliation(s)
- LaTisha V Moody
- Animal Care Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California
| | - Yukiko Miyamoto
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California
| | - Jonathan Ang
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California
| | - Philip J Richter
- Animal Care Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California
| | - Lars Eckmann
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California;,
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