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Safari Z, Sadeghizadeh M, Zavaran Hosseini A, Hazrati A, Soudi S. Intra-abdominal transplantation of PLGA/PCL/M13 phage electrospun scaffold induces self-assembly of lymphoid tissue-like structure. Biomed Pharmacother 2024; 173:116382. [PMID: 38460368 DOI: 10.1016/j.biopha.2024.116382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024] Open
Abstract
Lymphoid organs are the main structural components of the immune system. In the current research, the mixture of poly lactic-co-glycolic acid (PLGA), polycaprolactone (PCL), and M13 phage or its RGD-modified form was used in the construction of a fibrillar scaffold using the electrospinning method. The constructs were transplanted intra-abdominally and examined for the formation of lymphoid-like tissues at different time intervals. The confocal and scanning electron microscopy demonstrate that M13 phage-containing scaffolds provide a suitable environment for lymph node-isolated fibroblasts. Morphological analysis demonstrate the formation of lymph node-like tissues in the M13 phage-containing scaffolds after transplantation. Histological analysis confirm both blood and lymph angiogenesis in the implanted construct and migration of inflammatory cells to the M13 phage-containing scaffolds. In addition, flow cytometry and immunohistochemistry analysis showed the homing and compartmentalization of dendritic cells (DCs), B and T lymphocytes within the PLGA/PCL/M13 phage-RGD based scaffolds and similar to what is seen in the mouse lymphoid tissues. It seems that the application of M13 phage could improve the generation of functional lymphoid tissues in the electrospun scaffolds and could be used for lymphoid tissue regeneration.
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Affiliation(s)
- Zohreh Safari
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ahmad Zavaran Hosseini
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Hazrati
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Soudi
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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2
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Wiebe KG, Cook BWM, Lightly TJ, Court DA, Theriault SS. Investigation into scalable and efficient enterotoxigenic Escherichia coli bacteriophage production. Sci Rep 2024; 14:3618. [PMID: 38351153 PMCID: PMC10864315 DOI: 10.1038/s41598-024-53276-w] [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: 06/27/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
As the demand for bacteriophage (phage) therapy increases due to antibiotic resistance in microbial pathogens, strategies and methods for increased efficiency, large-scale phage production need to be determined. To date, very little has been published on how to establish scalable production for phages, while achieving and maintaining a high titer in an economical manner. The present work outlines a phage production strategy using an enterotoxigenic Escherichia coli-targeting phage, 'Phage75', and accounts for the following variables: infection load, multiplicity of infection, temperature, media composition, harvest time, and host bacteria. To streamline this process, variables impacting phage propagation were screened through a high-throughput assay monitoring optical density at 600 nm (OD600) to indirectly infer phage production from host cell lysis. Following screening, propagation conditions were translated in a scalable fashion in shake flasks at 0.01 L, 0.1 L, and 1 L. A final, proof-of-concept production was then carried out in a CellMaker bioreactor to represent practical application at an industrial level. Phage titers were obtained in the range of 9.5-10.1 log10 PFU/mL with no significant difference between yields from shake flasks and CellMaker. Overall, this suggests that the methodology for scalable processing is reliable for translating into large-scale phage production.
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Affiliation(s)
- Katie G Wiebe
- Cytophage Technologies Inc., Winnipeg, MB, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | | | | | - Deborah A Court
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Steven S Theriault
- Cytophage Technologies Inc., Winnipeg, MB, Canada.
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.
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3
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Chang C, Guo W, Yu X, Guo C, Zhou N, Guo X, Huang RL, Li Q, Zhu Y. Engineered M13 phage as a novel therapeutic bionanomaterial for clinical applications: From tissue regeneration to cancer therapy. Mater Today Bio 2023; 20:100612. [PMID: 37063776 PMCID: PMC10102448 DOI: 10.1016/j.mtbio.2023.100612] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
Bacteriophages (phages) are nanostructured viruses with highly selective antibacterial properties that have gained attention beyond eliminating bacteria. Specifically, M13 phages are filamentous phages that have recently been studied in various aspects of nanomedicine due to their biological advantages and more compliant engineering capabilities over other phages. Having nanofiber-like morphology, M13 phages can reach varied target sites and self-assemble into multidimensional scaffolds in a relatively safe and stable way. In addition, genetic modification of the coat proteins enables specific display of peptides and antibodies on the phages, allowing for precise and individualized medicine. M13 phages have also been subjected to novel engineering approaches, including phage-based bionanomaterial engineering and phage-directed nanomaterial combinations that enhance the bionanomaterial properties of M13 phages. In view of these features, researchers have been able to utilize M13 phages for therapeutic applications such as drug delivery, biodetection, tissue regeneration, and targeted cancer therapy. In particular, M13 phages have been utilized as a novel bionanomaterial for precisely mimicking natural tissue environment in order to overcome the shortage in tissue and organ donors. Hence, in this review, we address the recent studies and advances of using M13 phages in the field of nanomedicine as therapeutic agents based upon their characteristics as novel bionanomaterial with biomolecules displayed. This paper also emphasizes the novel engineering approach that enhances M13 phage's bionanomaterial capabilities. Current limitations and future approaches are also discussed to provide insight in further progress for M13 phage-based clinical applications.
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Affiliation(s)
- Cheng Chang
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Wennan Guo
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Xinbo Yu
- Second Dental Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201999, China
| | - Chaoyi Guo
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Nan Zhou
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Ru-Lin Huang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Corresponding author.
| | - Qingtian Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Corresponding author.
| | - Yongzhang Zhu
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
- Corresponding author.
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4
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Safari Z, Sadeghizadeh M, Asgaritarghi G, Bardania H, Sadeghizadeh D, Soudi S. M13 phage coated surface elicits an anti-inflammatory response in BALB/c and C57BL/6 peritoneal macrophages. Int Immunopharmacol 2022; 107:108654. [PMID: 35421683 DOI: 10.1016/j.intimp.2022.108654] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/22/2022]
Abstract
Bacteriophages are one of the viral components of the human microbiome. M13 phages have recently been considered for immunotherapy because they can be detected by immune cells and stimulated immune responses. Macrophages are essential innate immune cells that respond to stimuli and direct subsequent immune responses. Therefore, it is crucial to evaluate the immunomodulatory effect of phage on macrophage function. For this purpose, peritoneal macrophages from BALB/c and C57BL/6 mice were cultured on the M13 phage, M13 phage-RGD, gelatin-coated, and un-coated wells. Then macrophages were examined for morphological characteristics, L. arginine metabolism, redox potential, inflammatory cytokine production, and phagocytic activity after two and seven days of culture. We observed that M13 phage-coated surfaces induced anti-inflammatory cytokines production and reduced inflammatory cytokines level of BALB/c and C57BL/6 macrophages at the steady-state and post LPS stimulation. In addition, L. arginine metabolism and phagocytic activity of macrophages were directed to the M2 phenotype by induction of arginase-1 and efferocytosis in the M13 phage-containing groups, respectively. The present study confirms the M13 phage's ability to polarize macrophages toward the M2 phenotype. However, using M13 phage in treating inflammatory diseases in animal models could determine their immunotherapy capacity in the future.
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Affiliation(s)
- Zohreh Safari
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Golareh Asgaritarghi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hassan Bardania
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Dina Sadeghizadeh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sara Soudi
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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Silva J, Dias R, Junior JI, Marcelino M, Silva M, Carmo A, Sousa M, Silva C, de Paula S. A Rapid Method for Performing a Multivariate Optimization of Phage Production Using the RCCD Approach. Pathogens 2021; 10:1100. [PMID: 34578135 PMCID: PMC8468216 DOI: 10.3390/pathogens10091100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 01/15/2023] Open
Abstract
Bacteriophages can be used in various applications, from the classical approach as substitutes for antibiotics (phage therapy) to new biotechnological uses, i.e., as a protein delivery vehicle, a diagnostic tool for specific strains of bacteria (phage typing), or environmental bioremediation. The demand for bacteriophage production increases daily, and studies that improve these production processes are necessary. This study evaluated the production of a T4-like bacteriophage vB_EcoM-UFV09 (an E. coli-infecting phage with high potential for reducing environmental biofilms) in seven types of culture media (Luria-Bertani broth and the M9 minimal medium with six different carbon sources) employing four cultivation variables (temperature, incubation time, agitation, and multiplicity of infection). For this purpose, the rotatable central composite design (RCCD) methodology was used, combining and comparing all parameters to determine the ideal conditions for starting to scale up the production process. We used the RCCD to set up the experimental design by combining the cultivation parameters in a specific and systematic way. Despite the high number of conditions evaluated, the results showed that when specific conditions were utilized, viral production was effective even when using a minimal medium, such as M9/glucose, which is less expensive and can significantly reduce costs during large-scale phage production.
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Affiliation(s)
- Jessica Silva
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - Roberto Dias
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - José Ivo Junior
- Department of Statistics, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
| | - Maraísa Marcelino
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - Mirelly Silva
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - Adriele Carmo
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
| | - Maira Sousa
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
- Leopoldo Américo Miguez de Mello Research Center (CENPES), Petrobras, Rio de Janeiro 20230-010, Brazil
| | - Cynthia Silva
- Department of Microbiology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
| | - Sergio de Paula
- Laboratory of Molecular Immunovirology, Department of General Biology, Federal University of Viçosa, Viçosa, Minas Gerais 36570-900, Brazil; (J.S.); (R.D.); (M.M.); (M.S.); (A.C.); (M.S.)
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Zamyatina AV, Rudenko NV, Karatovskaya AP, Shepelyakovskaya AO, Siunov AV, Andreeva-Kovalevskaya ZI, Nagel AS, Salyamov VI, Kolesnikov AS, Brovko FA, Solonin AS. Monoclonal Antibody HlyIIC‑15 to C-End Domain HlyII B. cereus Interacts with the Trombin Recognition Site. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020; 46:1214-1220. [PMID: 33390685 PMCID: PMC7768993 DOI: 10.1134/s1068162020060382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/23/2022]
Abstract
Among the panel of monoclonal antibodies to the recombinant protein HlyIICTD Bacillus cereus an antibody was found capable of forming an immune complex with a thrombin recognition region, the amino acid sequence of which is located inside the recombinant HlyIICTD. Localization of the epitope was carried out using peptide phage display methods, as well as enzyme immunoassay and immunoblotting for interaction with recombinant proteins, either containing or not containing individual components HlyIICTD. The identified epitope is located in the region of the thrombin site and retains the ability to interact with the antibody after the proteolyotic attack of the protein by thrombin.
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Affiliation(s)
- A. V. Zamyatina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Pushchino Branch, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
- Pushchino State Natural Science Institute, Pushchino, Moscow oblast 142290 Russia
| | - N. V. Rudenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Pushchino Branch, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
| | - A. P. Karatovskaya
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Pushchino Branch, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
| | - A. O. Shepelyakovskaya
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Pushchino Branch, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
| | - A. V. Siunov
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
| | - Zh. I. Andreeva-Kovalevskaya
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
| | - A. S. Nagel
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
| | - V. I. Salyamov
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
| | - A. S. Kolesnikov
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
| | - F. A. Brovko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Pushchino Branch, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
- Pushchino State Natural Science Institute, Pushchino, Moscow oblast 142290 Russia
| | - A. S. Solonin
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino, Moscow oblast 142290 Russia
- Pushchino State Natural Science Institute, Pushchino, Moscow oblast 142290 Russia
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7
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Rudenko N, Nagel A, Zamyatina A, Karatovskaya A, Salyamov V, Andreeva-Kovalevskaya Z, Siunov A, Kolesnikov A, Shepelyakovskaya A, Boziev K, Melnik B, Brovko F, Solonin A. A Monoclonal Antibody against the C-Terminal Domain of Bacillus cereus Hemolysin II Inhibits HlyII Cytolytic Activity. Toxins (Basel) 2020; 12:E806. [PMID: 33352744 PMCID: PMC7767301 DOI: 10.3390/toxins12120806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/19/2020] [Accepted: 12/16/2020] [Indexed: 01/13/2023] Open
Abstract
Bacillus cereus is the fourth most common cause of foodborne illnesses that produces a variety of pore-forming proteins as the main pathogenic factors. B. cereus hemolysin II (HlyII), belonging to pore-forming β-barrel toxins, has a C-terminal extension of 94 amino acid residues designated as HlyIICTD. An analysis of a panel of monoclonal antibodies to the recombinant HlyIICTD protein revealed the ability of the antibody HlyIIC-20 to inhibit HlyII hemolysis. A conformational epitope recognized by HlyIIC-20 was found. by the method of peptide phage display and found that it is localized in the N-terminal part of HlyIICTD. The HlyIIC-20 interacted with a monomeric form of HlyII, thus suppressing maturation of the HlyII toxin. Protection efficiencies of various B. cereus strains against HlyII were different and depended on the epitope amino acid composition, as well as, insignificantly, on downstream amino acids. Substitution of L324P and P324L in the hemolysins ATCC14579T and B771, respectively, determined the role of leucine localized to the epitope in suppressing the hemolysis by the antibody. Pre-incubation of HlyIIC-20 with HlyII prevented the death of mice up to an equimolar ratio. A strategy of detecting and neutralizing the toxic activity of HlyII could provide a tool for monitoring and reducing B. cereus pathogenicity.
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Affiliation(s)
- Natalia Rudenko
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.Z.); (A.K.); (A.S.); (K.B.); (F.B.)
| | - Alexey Nagel
- FSBIS FRC Pushchino Scientific Centre of Biological Research, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.N.); (V.S.); (Z.A.-K.); (A.S.); (A.K.); (A.S.)
| | - Anna Zamyatina
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.Z.); (A.K.); (A.S.); (K.B.); (F.B.)
- Pushchino State Institute of Natural Sciences, 3 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia
| | - Anna Karatovskaya
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.Z.); (A.K.); (A.S.); (K.B.); (F.B.)
| | - Vadim Salyamov
- FSBIS FRC Pushchino Scientific Centre of Biological Research, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.N.); (V.S.); (Z.A.-K.); (A.S.); (A.K.); (A.S.)
| | - Zhanna Andreeva-Kovalevskaya
- FSBIS FRC Pushchino Scientific Centre of Biological Research, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.N.); (V.S.); (Z.A.-K.); (A.S.); (A.K.); (A.S.)
| | - Alexander Siunov
- FSBIS FRC Pushchino Scientific Centre of Biological Research, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.N.); (V.S.); (Z.A.-K.); (A.S.); (A.K.); (A.S.)
| | - Alexander Kolesnikov
- FSBIS FRC Pushchino Scientific Centre of Biological Research, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.N.); (V.S.); (Z.A.-K.); (A.S.); (A.K.); (A.S.)
| | - Anna Shepelyakovskaya
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.Z.); (A.K.); (A.S.); (K.B.); (F.B.)
| | - Khanafiy Boziev
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.Z.); (A.K.); (A.S.); (K.B.); (F.B.)
| | - Bogdan Melnik
- Protein Institute of the Russian Academy of Sciences, 4 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia;
| | - Fedor Brovko
- Pushchino Branch, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 6 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.Z.); (A.K.); (A.S.); (K.B.); (F.B.)
| | - Alexander Solonin
- FSBIS FRC Pushchino Scientific Centre of Biological Research, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, 142290 Pushchino, Moscow Region, Russia; (A.N.); (V.S.); (Z.A.-K.); (A.S.); (A.K.); (A.S.)
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8
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Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies. Molecules 2020; 25:molecules25153386. [PMID: 32722650 PMCID: PMC7435391 DOI: 10.3390/molecules25153386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.
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9
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Shepherd TR, Du RR, Huang H, Wamhoff EC, Bathe M. Bioproduction of pure, kilobase-scale single-stranded DNA. Sci Rep 2019; 9:6121. [PMID: 30992517 PMCID: PMC6467869 DOI: 10.1038/s41598-019-42665-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/05/2019] [Indexed: 11/13/2022] Open
Abstract
Scalable production of kilobase single-stranded DNA (ssDNA) with sequence control has applications in therapeutics, gene synthesis and sequencing, scaffolded DNA origami, and archival DNA memory storage. Biological production of circular ssDNA (cssDNA) using M13 addresses these needs at low cost. However, one unmet goal is to minimize the essential protein coding regions of the exported DNA while maintaining its infectivity and production purity to produce sequences less than 3,000 nt in length, relevant to therapeutic and materials science applications. Toward this end, synthetic miniphage with inserts of custom sequence and size offers scalable, low-cost synthesis of cssDNA at milligram and higher scales. Here, we optimize growth conditions using an E. coli helper strain combined with a miniphage genome carrying only an f1 origin and a β-lactamase-encoding (bla) antibiotic resistance gene, enabling isolation of pure cssDNA with a minimum sequence genomic length of 1,676 nt, without requiring additional purification from contaminating DNA. Low-cost scalability of isogenic, custom-length cssDNA is demonstrated for a sequence of 2,520 nt using a bioreactor, purified with low endotoxin levels (<5 E.U./ml). We apply these exonuclease-resistant cssDNAs to the self-assembly of wireframe DNA origami objects and to encode digital information on the miniphage genome for biological amplification.
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Affiliation(s)
- Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Rebecca R Du
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hellen Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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10
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Abstract
A plaque of bacteriophage M13 derives from infection of a single bacterium by a single virus particle. The progeny particles infect neighboring bacteria, which, in turn, release another generation of daughter virus particles. If the bacteria are growing in semisolid medium (e.g., containing agar or agarose), then the diffusion of the progeny particles is limited. Cells infected with bacteriophage M13 are not killed, but have a longer generation time than uninfected Escherichia coli In consequence, plaques appear as areas of slower-growing cells on a faster-growing lawn of bacterial cells. This protocol describes plating of bacteriophage M13 stocks. Plaques are readily detectable on top agar after 4-8 h of incubation at 37°C.
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Kick B, Hensler S, Praetorius F, Dietz H, Weuster-Botz D. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnol Bioeng 2016; 114:777-784. [PMID: 27748519 DOI: 10.1002/bit.26200] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/30/2016] [Accepted: 10/10/2016] [Indexed: 01/18/2023]
Abstract
The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection, and specific growth rate. The specific growth rate and the multiplicity of infection were identified as the crucial state variables that influence phage amplification rate on one hand and the concentration of produced ssDNA on the other hand. Using a growth rate of 0.15 h-1 and a multiplicity of infection of 0.05 pfu cfu-1 in the fed-batch production process, the concentration of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced by 54% to 590 mg L-1 . Thus, our results help enabling M13 production for industrial uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777-784. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Benjamin Kick
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, Garching, 85748, Germany
| | - Samantha Hensler
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, Garching, 85748, Germany
| | - Florian Praetorius
- Physik Department and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Hendrik Dietz
- Physik Department and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, Garching, 85748, Germany
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12
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Kick B, Praetorius F, Dietz H, Weuster-Botz D. Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami. NANO LETTERS 2015; 15:4672-6. [PMID: 26028443 PMCID: PMC4532261 DOI: 10.1021/acs.nanolett.5b01461] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/28/2015] [Indexed: 05/20/2023]
Abstract
Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 10(14) plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale.
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Affiliation(s)
- Benjamin Kick
- Institute of Biochemical
Engineering, Technische Universität
München, Boltzmannstr.
15, 85748 Garching, Germany
| | - Florian Praetorius
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical
Engineering, Technische Universität
München, Boltzmannstr.
15, 85748 Garching, Germany
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13
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Reddy PT, Prasad CR, Reddy PH, Reeder D, McKenney K, Jaffe H, Dimitrova MN, Ginsburg A, Peterkofsky A, Murthy PS. Cloning and expression of the gene for a novel protein from Mycobacterium smegmatis with functional similarity to eukaryotic calmodulin. J Bacteriol 2003; 185:5263-8. [PMID: 12923099 PMCID: PMC180971 DOI: 10.1128/jb.185.17.5263-5268.2003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A calmodulin-like protein (CAMLP) from Mycobacterium smegmatis was purified to homogeneity and partially sequenced; these data were used to produce a full-length clone, whose DNA sequence contained a 55-amino-acid open reading frame. M. smegmatis CAMLP, expressed in Escherichia coli, exhibited properties characteristic of eukaryotic calmodulin: calcium-dependent stimulation of eukaryotic phosphodiesterase, which was inhibited by the calmodulin antagonist trifluoperazine, and reaction with anti-bovine brain calmodulin antibodies. Consistent with the presence of nine acidic amino acids (16%) in M. smegmatis CAMLP, there is one putative calcium-binding domain in this CAMLP, compared to four such domains for eukaryotic calmodulin, reflecting the smaller molecular size (approximately 6 kDa) of M. smegmatis CAMLP. Ultracentrifugation and mass spectral studies excluded the possibility that calcium promotes oligomerization of purified M. smegmatis CAMLP.
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Affiliation(s)
- Prasad T Reddy
- Bioprocess Engineering Group, Biotechnology Division, Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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