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Saroha P, Patil RS, Rathore AS. Recent advancements in soluble expression of recombinant antibody fragments in microbial host systems. Prep Biochem Biotechnol 2024:1-10. [PMID: 39196757 DOI: 10.1080/10826068.2024.2394446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Recombinant fabs dominate the pharmaceutical pipelines today with microbial host systems continuing to be a major contributor toward their production. Escherichia coli is a versatile host for recombinant protein expression due to its simplicity, affordability, and ability to be cultivated at high cell density. It is particularly suitable for non-glycosylated proteins and small proteins. Despite the aforementioned benefits, the use of E. coli as the host for the synthesis of recombinant antibody fragments often suffers from low yield and reduced activity. In most cases, proteins are expressed as inclusion bodies and need to undergo refolding to achieve their active forms and this refolding step is generally low-yielding. In this article, we review the various approaches that researchers have taken to enhance the production of recombinant antibody fragments in E. coli. Molecular biology-oriented approaches such as cloning, chaperone-mediated folding, and host cell screening as well as process optimization involving examination of process parameters, media, and feeding have been addressed.
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Affiliation(s)
- Preeti Saroha
- Department of Chemical Engineering, Indian Institute of Technology, New Delhi, India
| | - Rucha S Patil
- Department of Chemical Engineering, Indian Institute of Technology, New Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology, New Delhi, India
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2
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Cronan JE. Two neglected but valuable genetic tools for Escherichia coli and other bacteria: In vivo cosmid packaging and inducible plasmid replication. Mol Microbiol 2023; 120:783-790. [PMID: 37770255 DOI: 10.1111/mmi.15171] [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: 07/17/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 09/30/2023]
Abstract
In physiology and synthetic biology, it can be advantageous to introduce a gene into a naive bacterial host under conditions in which all cells receive the gene and remain fully functional. This cannot be done by the usual chemical transformation and electroporation methods due to low efficiency and cell death, respectively. However, in vivo packaging of plasmids (called cosmids) that contain the 223 bp cos site of phage λ results in phage particles that contain concatemers of the cosmid that can be transduced into all cells of a culture. An historical shortcoming of in vivo packaging of cosmids was inefficient packaging and contamination of the particles containing cosmid DNA with a great excess of infectious λ phage. Manipulation of the packaging phage and the host has eliminated these shortcomings resulting in particles that contain only cosmid DNA. Plasmids have the drawback that they can be difficult to remove from cells. Plasmids with conditional replication provide a means to "cure" plasmids from cells. The prevalent conditional replication plasmids are temperature-sensitive plasmids, which are cured at high growth temperature. However, inducible replication plasmids are in some cases more useful, especially since this approach has been applied to plasmids having diverse replication and compatibility properties.
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Affiliation(s)
- John E Cronan
- Departments of Microbiology and Biochemistry, University of Illinois, Urbana, Illinois, USA
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Turco F, Garavaglia M, Van Houdt R, Hill P, Rawson FJ, Kovacs K. Synthetic Biology Toolbox, Including a Single-Plasmid CRISPR-Cas9 System to Biologically Engineer the Electrogenic, Metal-Resistant Bacterium Cupriavidus metallidurans CH34. ACS Synth Biol 2022; 11:3617-3628. [PMID: 36278822 PMCID: PMC9680026 DOI: 10.1021/acssynbio.2c00130] [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] [Indexed: 01/27/2023]
Abstract
Cupriavidus metallidurans CH34 exhibits extraordinary metabolic versatility, including chemolithoautotrophic growth; degradation of BTEX (benzene, toluene, ethylbenzene, xylene); high resistance to numerous metals; biomineralization of gold, platinum, silver, and uranium; and accumulation of polyhydroxybutyrate (PHB). These qualities make it a valuable host for biotechnological applications such as bioremediation, bioprocessing, and the generation of bioelectricity in microbial fuel cells (MFCs). However, the lack of genetic tools for strain development and studying its fundamental physiology represents a bottleneck to boosting its commercial applications. In this study, inducible and constitutive promoter libraries were built and characterized, providing the first comprehensive list of biological parts that can be used to regulate protein expression and optimize the CRISPR-Cas9 genome editing tools for this host. A single-plasmid CRISPR-Cas9 system that can be delivered by both conjugation and electroporation was developed, and its efficiency was demonstrated by successfully targeting the pyrE locus. The CRISPR-Cas9 system was next used to target candidate genes encoding type IV pili, hypothesized by us to be involved in extracellular electron transfer (EET) in this organism. Single and double deletion strains (ΔpilA, ΔpilE, and ΔpilAE) were successfully generated. Additionally, the CRISPR-Cas9 tool was validated for constructing genomic insertions (ΔpilAE::gfp and ΔpilAE::λPrgfp). Finally, as type IV pili are believed to play an important role in extracellular electron transfer to solid surfaces, C. metallidurans CH34 ΔpilAE was further studied by means of cyclic voltammetry using disposable screen-printed carbon electrodes. Under these conditions, we demonstrated that C. metallidurans CH34 could generate extracellular currents; however, no difference in the intensity of the current peaks was found in the ΔpilAE double deletion strain when compared to the wild type. This finding suggests that the deleted type IV pili candidate genes are not involved in extracellular electron transfer under these conditions. Nevertheless, these experiments revealed the presence of different redox centers likely to be involved in both mediated electron transfer (MET) and direct electron transfer (DET), the first interpretation of extracellular electron transfer mechanisms in C. metallidurans CH34.
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Affiliation(s)
- Federico Turco
- School of Pharmacy,
Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Marco Garavaglia
- BBSRC/EPSRC Synthetic Biology Research
Centre, School of Life Sciences, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
| | - Phil Hill
- School
of Biosciences, The University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Frankie J. Rawson
- Bioelectronics Laboratory, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Katalin Kovacs
- Division of Molecular Therapeutics and Formulations,
School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom,
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Lee J. Lessons from Clostridial Genetics: Toward Engineering Acetogenic Bacteria. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-021-0062-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Backes N, Phillips GJ. Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales. EcoSal Plus 2021; 9:eESP00062020. [PMID: 34125584 PMCID: PMC11163844 DOI: 10.1128/ecosalplus.esp-0006-2020] [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: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/20/2022]
Abstract
Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.
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Affiliation(s)
- Nicholas Backes
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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Li S, Wen Z, Ghalandari B, Zhou T, Warden AR, Zhang T, Dai P, Yu Y, Guo W, Liu M, Xie H, Ding X. Single-Cell Immunoblotting based on a Photoclick Hydrogel Enables High-Throughput Screening and Accurate Profiling of Exogenous Gene Expression. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101108. [PMID: 33899289 DOI: 10.1002/adma.202101108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Fast and accurate profiling of exogenous gene expression in host cells is crucial for studying gene function in cellular and molecular biology, but still faces the challenge of incomplete co-expression of reporter genes and target genes. Here, a single-cell transfection analysis chip (scTAC) is presented, which is based on the in situ microchip immunoblotting method, for rapid and accurate analysis of exogenous gene expression in thousands of individual host cells. scTAC not only can assign information of exogenous gene activity to specific transfected cells, but enables the acquisition of continuous protein expression even in low co-expression scenarios. It is demonstrated that scTAC can reveal the relationship of expression level between reporter genes and target genes, which is helpful for evaluating transient transfection strategy efficiency. The advantages of this method for the study of fusion protein expression and downstream protein expression in signaling pathway in rare cells are shown. Empirically, an EGFP-TSPAN8 fusion plasmid is transfected into MCF-7 breast cancer cells and the expressions of two cancer stemness biomarkers (ALDHA1 and SOX2) are analyzed. The scTAC method clearly reveals an interesting phenomenon that transfected adherent MCF-7 cells exhibit some stem cell characteristics, but they do not have stem cell appearance.
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Affiliation(s)
- Shanhe Li
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ze Wen
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Behafarid Ghalandari
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Tianhao Zhou
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Antony R Warden
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ting Zhang
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Peng Dai
- Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Youyi Yu
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenke Guo
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Mofang Liu
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Haiyang Xie
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
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Wang J, Sui X, Ding Y, Fu Y, Feng X, Liu M, Zhang Y, Xian M, Zhao G. A fast and robust iterative genome-editing method based on a Rock-Paper-Scissors strategy. Nucleic Acids Res 2021; 49:e12. [PMID: 33270888 PMCID: PMC7826264 DOI: 10.1093/nar/gkaa1141] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/28/2020] [Accepted: 11/07/2020] [Indexed: 01/22/2023] Open
Abstract
The production of optimized strains of a specific phenotype requires the construction and testing of a large number of genome modifications and combinations thereof. Most bacterial iterative genome-editing methods include essential steps to eliminate selection markers, or to cure plasmids. Additionally, the presence of escapers leads to time-consuming separate single clone picking and subsequent cultivation steps. Herein, we report a genome-editing method based on a Rock-Paper-Scissors (RPS) strategy. Each of three constructed sgRNA plasmids can cure, or be cured by, the other two plasmids in the system; plasmids from a previous round of editing can be cured while the current round of editing takes place. Due to the enhanced curing efficiency and embedded double check mechanism, separate steps for plasmid curing or confirmation are not necessary, and only two times of cultivation are needed per genome-editing round. This method was successfully demonstrated in Escherichia coli and Klebsiella pneumoniae with both gene deletions and replacements. To the best of our knowledge, this is the fastest and most robust iterative genome-editing method, with the least times of cultivation decreasing the possibilities of spontaneous genome mutations.
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Affiliation(s)
- Jichao Wang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Xinyue Sui
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yamei Ding
- Institute of Oceanology, Chinese Academy of Sciences, 266071 Qingdao, China
| | - Yingxin Fu
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Xinjun Feng
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Min Liu
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
| | - Guang Zhao
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 266101 Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
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8
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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review. Gene 2020; 753:144813. [DOI: 10.1016/j.gene.2020.144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/26/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
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