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Omics-guided bacterial engineering of Escherichia coli ER2566 for recombinant protein expression. Appl Microbiol Biotechnol 2023; 107:853-865. [PMID: 36539564 PMCID: PMC9767853 DOI: 10.1007/s00253-022-12339-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
The goal of bacterial engineering is to rewire metabolic pathways to generate high-value molecules for various applications. However, the production of recombinant proteins is constrained by the complexity of the connections between cellular physiology and recombinant protein synthesis. Here, we used a rational and highly efficient approach to improve bacterial engineering. Based on the complete genome and annotation information of the Escherichia coli ER2566 strain, we compared the transcriptomic profiles of the strain under leaky expression and low temperature-induced stress. Combining the gene ontology (GO) enrichment terms and differentially expressed genes (DEGs) with higher expression, we selected and knocked out 36 genes to determine the potential impact of these genes on protein production. Deletion of bluF, cydA, mngR, and udp led to a significant decrease in soluble recombinant protein production. Moreover, at low-temperature induction, 4 DEGs (gntK, flgH, flgK, flgL) were associated with enhanced expression of the recombinant protein. Knocking out several motility-related DEGs (ER2666-ΔflgH-ΔflgL-ΔflgK) simultaneously improved the protein yield by 1.5-fold at 24 °C induction, and the recombinant strain had the potential to be applied in the expression studies of different exogenous proteins, aiming to improve the yields of soluble form to varying degrees in comparison to the ER2566 strain. Totally, this study focused on the anabolic and stress-responsive hub genes of the adaptation of E. coli to recombinant protein overexpression on the transcriptome level and constructs a series of engineering strains increasing the soluble protein yield of recombinant proteins which lays a solid foundation for the engineering of bacterial strains for recombinant technological advances. KEY POINTS: • Comparative transcriptome analysis shows host responses with altered induction stress. • Deletion of bluF, cydA, mngR, and udp genes was identified to significantly decrease the soluble recombinant protein productions. • Synchronal knockout of flagellar genes in E. coli can enhance recombinant protein yield up to ~ 1.5-fold at 24 °C induction. • Non-model bacterial strains can be re-engineered for recombinant protein expression.
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Koshy SM, Kincaid AE, Bartz JC. Transport of Prions in the Peripheral Nervous System: Pathways, Cell Types, and Mechanisms. Viruses 2022; 14:630. [PMID: 35337037 PMCID: PMC8954800 DOI: 10.3390/v14030630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 01/27/2023] Open
Abstract
Prion diseases are transmissible protein misfolding disorders that occur in animals and humans where the endogenous prion protein, PrPC, undergoes a conformational change into self-templating aggregates termed PrPSc. Formation of PrPSc in the central nervous system (CNS) leads to gliosis, spongiosis, and cellular dysfunction that ultimately results in the death of the host. The spread of prions from peripheral inoculation sites to CNS structures occurs through neuroanatomical networks. While it has been established that endogenous PrPC is necessary for prion formation, and that the rate of prion spread is consistent with slow axonal transport, the mechanistic details of PrPSc transport remain elusive. Current research endeavors are primarily focused on the cellular mechanisms of prion transport associated with axons. This includes elucidating specific cell types involved, subcellular machinery, and potential cofactors present during this process.
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Affiliation(s)
- Sam M. Koshy
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE 68178, USA;
| | - Anthony E. Kincaid
- Department of Pharmacy Science, School of Pharmacy and Health Professions, Creighton University, Omaha, NE 68178, USA;
| | - Jason C. Bartz
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE 68178, USA;
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Flow Cytometric Detection of PrP Sc in Neurons and Glial Cells from Prion-Infected Mouse Brains. J Virol 2017; 92:JVI.01457-17. [PMID: 29046463 DOI: 10.1128/jvi.01457-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/05/2017] [Indexed: 12/13/2022] Open
Abstract
In prion diseases, an abnormal isoform of prion protein (PrPSc) accumulates in neurons, astrocytes, and microglia in the brains of animals affected by prions. Detailed analyses of PrPSc-positive neurons and glial cells are required to clarify their pathophysiological roles in the disease. Here, we report a novel method for the detection of PrPSc in neurons and glial cells from the brains of prion-infected mice by flow cytometry using PrPSc-specific staining with monoclonal antibody (MAb) 132. The combination of PrPSc staining and immunolabeling of neural cell markers clearly distinguished neurons, astrocytes, and microglia that were positive for PrPSc from those that were PrPSc negative. The flow cytometric analysis of PrPSc revealed the appearance of PrPSc-positive neurons, astrocytes, and microglia at 60 days after intracerebral prion inoculation, suggesting the presence of PrPSc in the glial cells, as well as in neurons, from an early stage of infection. Moreover, the kinetic analysis of PrPSc revealed a continuous increase in the proportion of PrPSc-positive cells for all cell types with disease progression. Finally, we applied this method to isolate neurons, astrocytes, and microglia positive for PrPSc from a prion-infected mouse brain by florescence-activated cell sorting. The method described here enables comprehensive analyses specific to PrPSc-positive neurons, astrocytes, and microglia that will contribute to the understanding of the pathophysiological roles of neurons and glial cells in PrPSc-associated pathogenesis.IMPORTANCE Although formation of PrPSc in neurons is associated closely with neurodegeneration in prion diseases, the mechanism of neurodegeneration is not understood completely. On the other hand, recent studies proposed the important roles of glial cells in PrPSc-associated pathogenesis, such as the intracerebral spread of PrPSc and clearance of PrPSc from the brain. Despite the great need for detailed analyses of PrPSc-positive neurons and glial cells, methods available for cell type-specific analysis of PrPSc have been limited thus far to microscopic observations. Here, we have established a novel high-throughput method for flow cytometric detection of PrPSc in cells with more accurate quantitative performance. By applying this method, we succeeded in isolating PrPSc-positive cells from the prion-infected mouse brains via fluorescence-activated cell sorting. This allows us to perform further detailed analysis specific to PrPSc-positive neurons and glial cells for the clarification of pathological changes in neurons and pathophysiological roles of glial cells.
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Bradley SJ, Bourgognon JM, Sanger HE, Verity N, Mogg AJ, White DJ, Butcher AJ, Moreno JA, Molloy C, Macedo-Hatch T, Edwards JM, Wess J, Pawlak R, Read DJ, Sexton PM, Broad LM, Steinert JR, Mallucci GR, Christopoulos A, Felder CC, Tobin AB. M1 muscarinic allosteric modulators slow prion neurodegeneration and restore memory loss. J Clin Invest 2016; 127:487-499. [PMID: 27991860 PMCID: PMC5272187 DOI: 10.1172/jci87526] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 11/03/2016] [Indexed: 11/17/2022] Open
Abstract
The current frontline symptomatic treatment for Alzheimer's disease (AD) is whole-body upregulation of cholinergic transmission via inhibition of acetylcholinesterase. This approach leads to profound dose-related adverse effects. An alternative strategy is to selectively target muscarinic acetylcholine receptors, particularly the M1 muscarinic acetylcholine receptor (M1 mAChR), which was previously shown to have procognitive activity. However, developing M1 mAChR-selective orthosteric ligands has proven challenging. Here, we have shown that mouse prion disease shows many of the hallmarks of human AD, including progressive terminal neurodegeneration and memory deficits due to a disruption of hippocampal cholinergic innervation. The fact that we also show that muscarinic signaling is maintained in both AD and mouse prion disease points to the latter as an excellent model for testing the efficacy of muscarinic pharmacological entities. The memory deficits we observed in mouse prion disease were completely restored by treatment with benzyl quinolone carboxylic acid (BQCA) and benzoquinazoline-12 (BQZ-12), two highly selective positive allosteric modulators (PAMs) of M1 mAChRs. Furthermore, prolonged exposure to BQCA markedly extended the lifespan of diseased mice. Thus, enhancing hippocampal muscarinic signaling using M1 mAChR PAMs restored memory loss and slowed the progression of mouse prion disease, indicating that this ligand type may have clinical benefit in diseases showing defective cholinergic transmission, such as AD.
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Affiliation(s)
- Sophie J. Bradley
- The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Helen E. Sanger
- Eli Lilly and Co., Neuroscience, Windlesham, Surrey, United Kingdom
| | - Nicholas Verity
- MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
| | - Adrian J. Mogg
- Eli Lilly and Co., Neuroscience, Windlesham, Surrey, United Kingdom
| | - David J. White
- Central Research Facility, University of Leicester, Leicester, United Kingdom
| | - Adrian J. Butcher
- MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
| | - Julie A. Moreno
- MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
| | - Colin Molloy
- The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Jurgen Wess
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Robert Pawlak
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - David J. Read
- MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
| | - Patrick M. Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia
| | - Lisa M. Broad
- Eli Lilly and Co., Neuroscience, Windlesham, Surrey, United Kingdom
| | - Joern R. Steinert
- MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
| | - Giovanna R. Mallucci
- MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia
| | - Christian C. Felder
- Eli Lilly and Co., Neuroscience, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - Andrew B. Tobin
- The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Striebel JF, Race B, Chesebro B. Prion protein and susceptibility to kainate-induced seizures: genetic pitfalls in the use of PrP knockout mice. Prion 2013; 7:280-5. [PMID: 23851597 PMCID: PMC3904312 DOI: 10.4161/pri.25738] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Prion protein (PrP) is a cell surface glycoprotein which is required for susceptibility to prion infection and disease. However, PrP is expressed in many different cell types located in numerous organs. Therefore, in addition to its role in prion diseases, PrP may have a large variety of other biological functions involving the nervous system and other systems. We recently showed that susceptibility to kainate-induced seizures differed in Prnp−/− and Prnp+/+ mice on the C57BL/10SnJ background. However, in a genetic complementation experiment a PrP expressing transgene was not able to rescue the Prnp+/+ phenotype. Thus the apparent effect of PrP on seizures was actually due to genes flanking the Prnp−/− gene rather that the Prnp deletion itself. We discuss here several pitfalls in the use of Prnp−/− genotypes expressed in various mouse genetic backgrounds to determine the functions of PrP. In particular, the use of Prnp−/− mice with heterogeneous mixed genetic backgrounds may have weakened the conclusions of many previous experiments. Use of either co-isogenic mice or congenic mice with more homogeneous genetic backgrounds is now feasible. For congenic mice, the potential problem of flanking genes can be mitigated by the use of appropriate transgene rescue experiments to confirm the conclusions.
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Affiliation(s)
- James F Striebel
- Laboratory of Persistent Viral Diseases; Rocky Mountain Laboratories; National Institute of Allergy and Infectious Diseases; Hamilton, MO USA
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