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Beyer JN, Serebrenik YV, Toy K, Najar MA, Raniszewski NR, Shalem O, Burslem GM. Intracellular Protein Editing to Enable Incorporation of Non-Canonical Residues into Endogenous Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602493. [PMID: 39026884 PMCID: PMC11257474 DOI: 10.1101/2024.07.08.602493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The ability to study proteins in a cellular context is crucial to our understanding of biology. Here, we report a new technology for "intracellular protein editing", drawing from intein- mediated protein splicing, genetic code expansion, and endogenous protein tagging. This protein editing approach enables us to rapidly and site specifically install residues and chemical handles into a protein of interest. We demonstrate the power of this protein editing platform to edit cellular proteins, inserting epitope peptides, protein-specific sequences, and non-canonical amino acids (ncAAs). Importantly, we employ an endogenous tagging approach to apply our protein editing technology to endogenous proteins with minimal perturbation. We anticipate that the protein editing technology presented here will be applied to a diverse set of problems, enabling novel experiments in live mammalian cells and therefore provide unique biological insights.
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2
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Kandarakov OF, Polyakova NS, Petrovskaya AV, Bruter AV, Belyavsky AV. CD52/FLAG and CD52/HA Fusion Proteins as Novel Magnetic Cell Selection Markers. Int J Mol Sci 2024; 25:6353. [PMID: 38928060 PMCID: PMC11203882 DOI: 10.3390/ijms25126353] [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: 04/29/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
At present, the magnetic selection of genetically modified cells is mainly performed with surface markers naturally expressed by cells such as CD4, LNGFR (low affinity nerve growth factor receptor), and MHC class I molecule H-2Kk. The disadvantage of such markers is the possibility of their undesired and poorly predictable expression by unmodified cells before or after cell manipulation, which makes it essential to develop new surface markers that would not have such a drawback. Earlier, modified CD52 surface protein variants with embedded HA and FLAG epitope tags (CD52/FLAG and CD52/HA) were developed by the group of Dr. Mazurov for the fluorescent cell sorting of CRISPR-modified cells. In the current study, we tested whether these markers can be used for the magnetic selection of transduced cells. For this purpose, appropriate constructs were created in MigR1-based bicistronic retroviral vectors containing EGFP and DsRedExpress2 as fluorescent reporters. Cytometric analysis of the transduced NIH 3T3 cell populations after magnetic selection evaluated the efficiency of isolation and purity of the obtained populations, as well as the change in the median fluorescence intensity (MFI). The results of this study demonstrate that the surface markers CD52/FLAG and CD52/HA can be effectively used for magnetic cell selection, and their efficiencies are comparable to that of the commonly used LNGFR marker. At the same time, the significant advantage of these markers is the absence of HA and FLAG epitope sequences in cellular proteins, which rules out the spurious co-isolation of negative cells.
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Affiliation(s)
- Oleg F. Kandarakov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia; (O.F.K.); (N.S.P.); (A.V.P.)
| | - Natalia S. Polyakova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia; (O.F.K.); (N.S.P.); (A.V.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Vavilov Str. 32, 119991 Moscow, Russia;
| | - Alexandra V. Petrovskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia; (O.F.K.); (N.S.P.); (A.V.P.)
| | - Alexandra V. Bruter
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Vavilov Str. 32, 119991 Moscow, Russia;
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Str. 34/5, 119334 Moscow, Russia
| | - Alexander V. Belyavsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia; (O.F.K.); (N.S.P.); (A.V.P.)
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3
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Shilleh AH, Viloria K, Broichhagen J, Campbell JE, Hodson DJ. GLP1R and GIPR expression and signaling in pancreatic alpha cells, beta cells and delta cells. Peptides 2024; 175:171179. [PMID: 38360354 DOI: 10.1016/j.peptides.2024.171179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/17/2024]
Abstract
Glucagon-like peptide-1 receptor (GLP1R) and glucose-dependent insulinotropic polypeptide receptor (GIPR) are transmembrane receptors involved in insulin, glucagon and somatostatin secretion from the pancreatic islet. Therapeutic targeting of GLP1R and GIPR restores blood glucose levels in part by influencing beta cell, alpha cell and delta cell function. Despite the importance of the incretin-mimetics for diabetes therapy, our understanding of GLP1R and GIPR expression patterns and signaling within the islet remain incomplete. Here, we present the evidence for GLP1R and GIPR expression in the major islet cell types, before addressing signaling pathway(s) engaged, as well as their influence on cell survival and function. While GLP1R is largely a beta cell-specific marker within the islet, GIPR is expressed in alpha cells, beta cells, and (possibly) delta cells. GLP1R and GIPR engage Gs-coupled pathways in most settings, although the exact outcome on hormone release depends on paracrine communication and promiscuous signaling. Biased agonism away from beta-arrestin is an emerging concept for improving therapeutic efficacy, and is also relevant for GLP1R/GIPR dual agonism. Lastly, dual agonists exert multiple effects on islet function through GIPR > GLP1R imbalance, increased GLP1R surface expression and cAMP signaling, as well as beneficial alpha cell-beta cell-delta cell crosstalk.
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Affiliation(s)
- Ali H Shilleh
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Katrina Viloria
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Jonathan E Campbell
- Duke Molecular Physiology Institute, USA; Department of Medicine, Division of Endocrinology, Duke University, Durham, NC, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
| | - David J Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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4
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Islam S, Gour J, Beer T, Tang HY, Cassel J, Salvino JM, Busino L. A Tandem-Affinity Purification Method for Identification of Primary Intracellular Drug-Binding Proteins. ACS Chem Biol 2024; 19:233-242. [PMID: 38271588 PMCID: PMC10878392 DOI: 10.1021/acschembio.3c00570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
In the field of drug discovery, understanding how small molecule drugs interact with cellular components is crucial. Our study introduces a novel methodology to uncover primary drug targets using Tandem Affinity Purification for identification of Drug-Binding Proteins (TAP-DBP). Central to our approach is the generation of a FLAG-hemagglutinin (HA)-tagged chimeric protein featuring the FKBP12(F36V) adaptor protein and the TurboID enzyme. Conjugation of drug molecules with the FKBP12(F36V) ligand allows for the coordinated recruitment of drug-binding partners effectively enabling in-cell TurboID-mediated biotinylation. By employing a tandem affinity purification protocol based on FLAG-immunoprecipitation and streptavidin pulldown, alongside mass spectrometry analysis, TAP-DBP allows for the precise identification of drug-primary binding partners. Overall, this study introduces a systematic, unbiased method for identification of drug-protein interactions, contributing a clear understanding of target engagement and drug selectivity to advance the mode of action of a drug in cells.
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Affiliation(s)
- Sehbanul Islam
- University
of Pennsylvania, Perelman School
of Medicine, Department of Cancer Biology, Philadelphia, Pennsylvania 19104, United States
| | - Jitendra Gour
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Thomas Beer
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Hsin-Yao Tang
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Joel Cassel
- Molecular
Screening and Protein Expression Shared Resource, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Joseph M. Salvino
- Medicinal
Chemistry and Molecular and Cellular Oncogenesis (MCO) Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Luca Busino
- University
of Pennsylvania, Perelman School
of Medicine, Department of Cancer Biology, Philadelphia, Pennsylvania 19104, United States
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5
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Si D, Li Q, Bao Y, Zhang J, Wang L. Fluorogenic and Cell-Permeable Rhodamine Dyes for High-Contrast Live-Cell Protein Labeling in Bioimaging and Biosensing. Angew Chem Int Ed Engl 2023; 62:e202307641. [PMID: 37483077 DOI: 10.1002/anie.202307641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 07/25/2023]
Abstract
The advancement of fluorescence microscopy techniques has opened up new opportunities for visualizing proteins and unraveling their functions in living biological systems. Small-molecule organic dyes, which possess exceptional photophysical properties, small size, and high photostability, serve as powerful fluorescent reporters in protein imaging. However, achieving high-contrast live-cell labeling of target proteins with conventional organic dyes remains a considerable challenge in bioimaging and biosensing due to their inadequate cell permeability and high background signal. Over the past decade, a novel generation of fluorogenic and cell-permeable dyes has been developed, which have substantially improved live-cell protein labeling by fine-tuning the reversible equilibrium between a cell-permeable, nonfluorescent spirocyclic state (unbound) and a fluorescent zwitterion (protein-bound) of rhodamines. In this review, we present the mechanism and design strategies of these fluorogenic and cell-permeable rhodamines, as well as their applications in bioimaging and biosensing.
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Affiliation(s)
- Dongjuan Si
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Quanlin Li
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Yifan Bao
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Jingye Zhang
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Lu Wang
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
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Simoens L, Fijalkowski I, Van Damme P. Exposing the small protein load of bacterial life. FEMS Microbiol Rev 2023; 47:fuad063. [PMID: 38012116 PMCID: PMC10723866 DOI: 10.1093/femsre/fuad063] [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: 05/09/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023] Open
Abstract
The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed range of small proteins, or sORF-encoded polypeptides (SEPs). In recent years, continuous efforts led to great improvements in the annotation and characterization of such proteins, yet many challenges remain to fully comprehend the pervasive nature of small proteins and their impact on bacterial biology. In this work, we review the recent developments in the dynamic field of bacterial genome reannotation, catalog the important biological roles carried out by small proteins and identify challenges obstructing the way to full understanding of these elusive proteins.
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Affiliation(s)
- Laure Simoens
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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7
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Veenstra BT, Veenstra TD. Proteomic applications in identifying protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:1-48. [PMID: 38220421 DOI: 10.1016/bs.apcsb.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
There are many things that can be used to characterize a protein. Size, isoelectric point, hydrophobicity, structure (primary to quaternary), and subcellular location are just a few parameters that are used. The most important feature of a protein, however, is its function. While there are many experiments that can indicate a protein's role, identifying the molecules it interacts with is probably the most definitive way of determining its function. Owing to technology limitations, protein interactions have historically been identified on a one molecule per experiment basis. The advent of high throughput multiplexed proteomic technologies in the 1990s, however, made identifying hundreds and thousands of proteins interactions within single experiments feasible. These proteomic technologies have dramatically increased the rate at which protein-protein interactions (PPIs) are discovered. While the improvement in mass spectrometry technology was an early driving force in the rapid pace of identifying PPIs, advances in sample preparation and chromatography have recently been propelling the field. In this chapter, we will discuss the importance of identifying PPIs and describe current state-of-the-art technologies that demonstrate what is currently possible in this important area of biological research.
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Affiliation(s)
- Benjamin T Veenstra
- Department of Math and Sciences, Cedarville University, Cedarville, OH, United States
| | - Timothy D Veenstra
- School of Pharmacy, Cedarville University, Cedarville, OH, United States.
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8
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Zhang Y, Zhao L, Wang Q, Zhang Z, Ren X, Yang X, Zeng S, Lv L, Zhao L, Su S, Chen X, Fu B. A novel epitope tag from rabies virus has versatile in vitro applications. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12546-9. [PMID: 37166480 DOI: 10.1007/s00253-023-12546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Fusion tag technology is an important tool for rapid separation, purification, and characterization of proteins. Combined with monoclonal antibodies, tag epitope systems can be rapidly adapted to many assay systems. A monoclonal antibody that reacts with the matrix protein of the rabies virus CVS-11 strain was reported. The epitope (termed M) targeted by this antibody contains only six amino acids. We examine whether this specific sequence epitope can be applied as a protein tag. We show ectopic expression of M-tagged proteins has little impact on cell viability or major signaling pathways. The M tag system can be used for western blotting, immunoprecipitation, immunofluorescence staining, and flow cytometry assays. The results indicate the specificity, sensitivity, and versatility of this novel epitope tag system are comparable to the widely used FLAG tag system, providing researchers with an additional tool for molecular analysis. KEY POINTS: • A short peptide (Pro Pro Tyr Asp Asp Asp) can be applied as a new tag. • The new epitope-tagging fusion system has no effect on the main cellular signaling pathway. • The epitope-tagging fusion system can be widely used for western blotting, immunoprecipitation, immunofluorescence, flow cytometry, etc.
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Affiliation(s)
- Yuelan Zhang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Lin Zhao
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Qinyang Wang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Zhuyou Zhang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xiaoyan Ren
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xue Yang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Shaowei Zeng
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Linyue Lv
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural Universitygrid, 35155.37, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoqi Chen
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Bishi Fu
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China.
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9
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Zhao J, Zhou P, Zhang L, Liu W, Liu W, Zhang Y, Li Y, Shi Z, Gao J. N-region of Cry1Ia: A novel fusion tag for Escherichia coli and Pichia pastoris. J Biotechnol 2023; 366:54-64. [PMID: 36822476 DOI: 10.1016/j.jbiotec.2023.02.006] [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: 11/29/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
Secretory signal peptides (SPs) can increase enhanced green fluorescent protein (eGFP) expression in cytosol. In this study, SPs Iasp (Cry1Ia), Vasp (Vip3A), and their local sequences were used as fusion tags to compare their effects on eGFP expression in Escherichia coli MC4100 and Pichia pastoris GS115. In E coli, the solubility was almost opposite between the proteins encoded by Vegfp and Iegfp. This may be because the overall hydrophobicity of the SPs differed. When the hydrophobic H-region and C-region were removed, the negative effects on eGFP solubility of the N-regions of both SPs (IaN and VN) were significantly reduced without compromise on the expression level. IaN promotes eGFP protein yield 7.1-fold more than Iasp, and using this peptide in tandem (Ia3N) further enhanced fluorescent fusion protein solubility with an efficacy similar to that of a polycationic tag. Furthermore, the GS-IaNeGFP strain produced the highest fluorescent signal intensity when these fusion proteins were expressed in P. pastoris, and the expression was higher than in other strains, including eGFP. In conclusion, we revealed the potential of the N-region of Iasp as a fusion tag in both prokaryotic and eukaryotic cells and further demonstrated the value of the N-regions of abundant SPs.
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Affiliation(s)
- Juanli Zhao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Pu Zhou
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Luyao Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Wenhui Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Wei Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Yuqi Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Yi Li
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China
| | - Zongyong Shi
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China.
| | - Jianhua Gao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong 030801, Shanxi, China.
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10
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Low TY, Lee PY. Tandem Affinity Purification (TAP) of Interacting Prey Proteins with FLAG- and HA-Tagged Bait Proteins. Methods Mol Biol 2023; 2690:69-80. [PMID: 37450137 DOI: 10.1007/978-1-0716-3327-4_6] [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] [Indexed: 07/18/2023]
Abstract
Proteins often interact with each other to form complexes and play functional roles in almost all cellular processes. The study of protein-protein interactions is therefore critical to understand protein function and biological pathways. Affinity Purification coupled with Mass Spectrometry (AP-MS) is an invaluable technique for identifying the interaction partners in protein complexes. In this approach, the protein of interest is fused to an affinity tag, followed by the expression and purification of the fusion protein. The affinity-purified sample is then analyzed by mass spectrometry to identify the interaction partners of the bait proteins. In this chapter, we detail the protocol for tandem affinity purification (TAP) based on the use of the FLAG (a fusion tag with peptide sequence DYKDDDDK) and hemagglutinin (HA) peptide epitopes. The immunoprecipitation using dual-affinity tags offers the advantage of increasing the specificity of the purification with lower nonspecific-background interactions.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
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11
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Hou Y, Cheng X, Witman GB. Direct in situ protein tagging in Chlamydomonas reinhardtii utilizing TIM, a method for CRISPR/Cas9-based targeted insertional mutagenesis. PLoS One 2022; 17:e0278972. [PMID: 36490276 PMCID: PMC9733891 DOI: 10.1371/journal.pone.0278972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Chlamydomonas reinhardtii is an important model organism for the study of many cellular processes, and protein tagging is an increasingly indispensable tool for these studies. To circumvent the disadvantages of conventional approaches in creating a tagged cell line, which involve transforming either a wild-type or null-mutant cell line with an exogenous DNA construct that inserts randomly into the genome, we developed a strategy to tag the endogenous gene in situ. The strategy utilizes TIM, a CRISPR/Cas9-based method for targeted insertional mutagenesis in C. reinhardtii. We have tested the strategy on two genes: LF5/CDKL5, lack of which causes a long-flagella phenotype, and Cre09.g416350/NAP1L1, which has not been studied previously in C. reinhardtii. We successfully tagged the C-terminus of wild-type LF5 with the hemagglutinin (HA) tag with an efficiency of 7.4%. Sequencing confirmed that these strains are correctly edited. Western blotting confirmed the expression of HA-tagged LF5, and immunofluorescence microscopy showed that LF5-HA is localized normally. These strains have normal length flagella and appear wild type. We successfully tagged the N-terminus of Cre09.g416350 with mNeonGreen-3xFLAG with an efficiency of 9%. Sequencing showed that the tag region in these strains is as expected. Western blotting confirmed the expression of tagged protein of the expected size in these strains, which appeared to have normal cell size, growth rate, and swimming speed. This is the first time that C. reinhardtii endogenous genes have been edited in situ to express a wild-type tagged protein. This effective, efficient, and convenient TIM-tagging strategy promises to be a useful tool for the study of nuclear genes, including essential genes, in C. reinhardtii.
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Affiliation(s)
- Yuqing Hou
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Xi Cheng
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - George B. Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
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12
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Application of ALFA-Tagging in the Nematode Model Organisms Caenorhabditis elegans and Pristionchus pacificus. Cells 2022; 11:cells11233875. [PMID: 36497133 PMCID: PMC9740511 DOI: 10.3390/cells11233875] [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: 10/15/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The detection, manipulation and purification of proteins is key in modern life sciences studies. To achieve this goal, a plethora of epitope tags have been employed in model organisms from bacteria to humans. Recently, the introduction of the rationally designed ALFA-tag resulted in a highly versatile tool with a very broad spectrum of potential applications. ALFA-tagged proteins can be detected by nanobodies, the single-domain antibodies of camelids, allowing for super-resolution microscopy and immunoprecipitation in biochemical applications. Here, we introduce ALFA-tagging into the two nematode model organisms Caenorhabditis elegans and Pristionchus pacificus. We show that the introduction of the DNA sequence, corresponding to the 13 amino acid sequence of the ALFA-tag, can easily be accommodated by CRISPR engineering. We provide examples of high-resolution protein expression in both nematodes. Finally, we use the GW182 ortholog Ppa-ain-1 to show successful pulldowns in P. pacificus. Thus, the ALFA-tag represents a novel epitope tag for nematode research with a broad spectrum of applications.
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13
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Stoyko D, Timothy O, Hernandez A, Konstantinidou P, Meng Q, Haase AD. CRISPR-Cas9 Genome Editing and Rapid Selection of Cell Pools. Curr Protoc 2022; 2:e624. [PMID: 36546759 PMCID: PMC9793982 DOI: 10.1002/cpz1.624] [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] [Indexed: 12/24/2022]
Abstract
The harnessing of the CRISPR-Cas9 system allows for quick and inexpensive genome editing in tissue culture models. Traditional CRISPR-Cas9 genome editing techniques rely on the ability of single progenitor cells to expand into new pools in a process known as clonal expansion. This is a significant technical challenge that is difficult to overcome for nontransformed cell culture models such as Drosophila ovarian somatic sheath cells (OSCs). OSCs are a unique ex vivo model for epigenetic regulation by PIWI-interacting RNAs (piRNAs) that establish restriction of mobile genetic elements in germ cells to protect genome integrity. Here, we provide a protocol to generate endogenously tagged proteins and gene knockouts without the need for clonal selection. We combine CRISPR-Cas genome editing and knockin of antibiotic selection markers to generate edited cell pools. At the example of Drosophila piwi in OSCs, we demonstrate a strategy that relies on the insertion of an artificial intron to accommodate a selection marker with minimal disturbance of the resulting mRNA. In brief, our donor cassette contains a peptide tag and an optimized intron that accommodates a selection marker driven by an independent promoter on the other genomic strand. The selection marker is transcribed as an independent mRNA, and the intron is efficiently removed from the mRNA encoding the endogenously tagged (endo-tagged) piwi gene. The endo-tagged Piwi protein is expressed at wild-type levels and appropriately localizes to the nucleus of OSCs. We also describe strategies for C-terminal tagging and generation of knockout alleles in OSCs and in human embryonic kidney cells, discuss different design strategies, and provide a plasmid toolkit (available at Addgene). Our protocol enables robust genome editing in OSCs for the first time and provides a simple and time-saving alternative for other cell culture systems. Published 2022. This article is a U.S. Government work and is in the public domain in the USA. Basic Protocol 1: Design and cloning of single-guide RNA plasmids Basic Protocol 2: Design and cloning of donor template plasmids for epitope tagging Alternate Protocol: Design and cloning of donor template plasmids for gene knockout Basic Protocol 3: Transfection and selection of edited cell pools.
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Affiliation(s)
- Daniel Stoyko
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - O Timothy
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Adrianna Hernandez
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702
| | - Parthena Konstantinidou
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Qingcai Meng
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Astrid D. Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
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14
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Malekos E, Carpenter S. Short open reading frame genes in innate immunity: from discovery to characterization. Trends Immunol 2022; 43:741-756. [PMID: 35965152 PMCID: PMC10118063 DOI: 10.1016/j.it.2022.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/27/2022]
Abstract
Next-generation sequencing (NGS) technologies have greatly expanded the size of the known transcriptome. Many newly discovered transcripts are classified as long noncoding RNAs (lncRNAs) which are assumed to affect phenotype through sequence and structure and not via translated protein products despite the vast majority of them harboring short open reading frames (sORFs). Recent advances have demonstrated that the noncoding designation is incorrect in many cases and that sORF-encoded peptides (SEPs) translated from these transcripts are important contributors to diverse biological processes. Interest in SEPs is at an early stage and there is evidence for the existence of thousands of SEPs that are yet unstudied. We hope to pique interest in investigating this unexplored proteome by providing a discussion of SEP characterization generally and describing specific discoveries in innate immunity.
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Affiliation(s)
- Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Susan Carpenter
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA; Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
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15
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Cabalteja CC, Sachdev S, Cheloha RW. Characterization of a Nanobody-Epitope Tag Interaction and Its Application for Receptor Engineering. ACS Chem Biol 2022; 17:2296-2303. [PMID: 35930411 PMCID: PMC10200313 DOI: 10.1021/acschembio.2c00407] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Peptide epitope tags offer a valuable means for detection and manipulation of protein targets for which high quality detection reagents are not available. Most commonly used epitope tags are bound by conventional, full-size antibodies (Abs). The complex architecture of Abs complicates their application in protein engineering and intracellular applications. To address these shortcomings, single domain antibodies (nanobodies, Nbs) that recognize short peptide epitopes have become increasingly prized. Here, we characterize the interaction between a Nb (Nb6E) and a 14-mer peptide epitope. We identify residues in the peptide epitope essential for high affinity binding. Using this information in combination with computational modeling we propose a mode of interaction between Nb6E and this epitope. We apply this nanobody-epitope pair to augment the potency of a ligand at an engineered adenosine A2A receptor. This characterization of the nanobody-epitope pair opens the door to diverse applications including mechanistic studies of the G protein-coupled receptor function.
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Affiliation(s)
- Chino C. Cabalteja
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
| | - Shivani Sachdev
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
| | - Ross W. Cheloha
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
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16
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Shoba VM, Munkanatta Godage DNP, Chaudhary SK, Deb A, Siriwardena SU, Choudhary A. Synthetic Reprogramming of Kinases Expands Cellular Activities of Proteins. Angew Chem Int Ed Engl 2022; 61:e202202770. [DOI: 10.1002/anie.202202770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 12/22/2022]
Affiliation(s)
- Veronika M. Shoba
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Dhanushka N. P. Munkanatta Godage
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Santosh K. Chaudhary
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Arghya Deb
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Sachini U. Siriwardena
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Divisions of Renal Medicine and Engineering Brigham and Women's Hospital Boston MA 02115 USA
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17
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Gao J, Ouyang C, Zhao J, Han Y, Guo Q, Liu X, Zhang T, Duan M, Wang X, Xu C. Coexpressing the Signal Peptide of Vip3A and the Trigger Factor of Bacillus thuringiensis Enhances the Production Yield and Solubility of eGFP in Escherichia coli. Front Microbiol 2022; 13:892428. [PMID: 35923407 PMCID: PMC9342664 DOI: 10.3389/fmicb.2022.892428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
Many fusion tags have been developed to improve the expression of recombinant proteins. Besides the translocation of cargo proteins, the signal peptides (SPs) of some secretory proteins, such as the ssTorA and Iasp, have been used as an inclusion body tag (IB-tag) or the recombinant expression enhancer in the cytosol of E. coli. In this study, the approach to utilize the SP of Vip3A (Vasp) from Bacillus thuringiensis (Bt) as a fusion tag was investigated. The results showed that either the Vasp or its predicted N- (VN), H- (VH), and C-regions (VC), as well as their combinations (VNH, VNC, and VHC), were able to significantly enhance the production yield of eGFP. However, the hydrophobic region of the Vasp (VH and/or VC) made more than half of the eGFP molecules aggregated (VeGFP, VHeGFP, VCeGFP, VNHeGFP, VNCeGFP, and VHCeGFP). Interestingly, the addition of the Bt trigger factor (BtTF) led to the neutralization of the negative impact and solubilization of the fusion proteins. Therefore, the coexpression of Vasp or its derivates with the chaperone BtTF could be a novel dual-enhancement system for the production yield and solubility of recombinant proteins. Notably, EcTF was unable to impact the solubility of Vasp or its derivates guided proteins, suggesting its different specificities on the recognition or interaction. Additionally, this study also suggested that the translocation of Vip3 in the host cell would be regulated by the BtTF-involved model.
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Affiliation(s)
- Jianhua Gao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Chunping Ouyang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Juanli Zhao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Yan Han
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Qinghua Guo
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Xuan Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Tianjiao Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Ming Duan
- Experimental Teaching Center, Shanxi Agricultural University, Jinzhong, China
| | - Xingchun Wang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
- Xingchun Wang
| | - Chao Xu
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Chao Xu
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18
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Kubitz L, Bitsch S, Zhao X, Schmitt K, Deweid L, Roehrig A, Barazzone EC, Valerius O, Kolmar H, Béthune J. Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells. Commun Biol 2022; 5:657. [PMID: 35788163 PMCID: PMC9253107 DOI: 10.1038/s42003-022-03604-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/20/2022] [Indexed: 12/11/2022] Open
Abstract
Proximity-dependent biotinylation (PDB) combined with mass spectrometry analysis has established itself as a key technology to study protein-protein interactions in living cells. A widespread approach, BioID, uses an abortive variant of the E. coli BirA biotin protein ligase, a quite bulky enzyme with slow labeling kinetics. To improve PDB versatility and speed, various enzymes have been developed by different approaches. Here we present a small-size engineered enzyme: ultraID. We show its practical use to probe the interactome of Argonaute-2 after a 10 min labeling pulse and expression at physiological levels. Moreover, using ultraID, we provide a membrane-associated interactome of coatomer, the coat protein complex of COPI vesicles. To date, ultraID is the smallest and most efficient biotin ligase available for PDB and offers the possibility of investigating interactomes at a high temporal resolution. A small-size engineered enzyme, ultraID, is presented for proximity-dependent biotinylation, that shows efficient labeling in mammalian cell culture, E. coli and S. cerevisiae.
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Affiliation(s)
- Lea Kubitz
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Sebastian Bitsch
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Xiyan Zhao
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Kerstin Schmitt
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Georg-August-University Göttingen, Göttingen, Germany
| | - Lukas Deweid
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.,Ferring Pharmaceuticals, Copenhagen, Denmark
| | - Amélie Roehrig
- Heidelberg University Biochemistry Center, Heidelberg, Germany.,Inserm UMRS1138 - FunGeST team, Paris, France
| | - Elisa Cappio Barazzone
- Heidelberg University Biochemistry Center, Heidelberg, Germany.,Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Oliver Valerius
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB) and Service Unit LCMS Protein Analytics, Georg-August-University Göttingen, Göttingen, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Julien Béthune
- Department of Biotechnology, Hamburg University of Applied Sciences, Hamburg, Germany.
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19
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Shoba VM, Munkanatta Godage DNP, Chaudhary SK, Deb A, Siriwardena SU, Choudhary A. Synthetic Reprogramming of Kinases Expands Cellular Activities of Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Veronika M. Shoba
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Dhanushka N. P. Munkanatta Godage
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Santosh K. Chaudhary
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Arghya Deb
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Sachini U. Siriwardena
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Divisions of Renal Medicine and Engineering Brigham and Women's Hospital Boston MA 02115 USA
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20
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Meng Q, Stoyko D, Andrews CM, Konstantinidou P, Genzor P, O T, Elchert AR, Benner L, Sobti S, Katz EY, Haase AD. Functional editing of endogenous genes through rapid selection of cell pools (Rapid generation of endogenously tagged genes in Drosophila ovarian somatic sheath cells). Nucleic Acids Res 2022; 50:e90. [PMID: 35639929 DOI: 10.1093/nar/gkac448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
The combination of genome-editing and epitope tagging provides a powerful strategy to study proteins with high affinity and specificity while preserving their physiological expression patterns. However, stably modifying endogenous genes in cells that do not allow for clonal selection has been challenging. Here, we present a simple and fast strategy to generate stable, endogenously tagged alleles in a non-transformed cell culture model. At the example of piwi in Drosophila ovarian somatic sheath cells, we show that this strategy enables the generation of an N-terminally tagged protein that emulates the expression level and subcellular localization of the wild type protein and forms functional Piwi-piRNA complexes. We further present a concise workflow to establish endogenously N-terminally and C-terminally tagged proteins, and knockout alleles through rapid selection of cell pools in fly and human models.
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Affiliation(s)
- Qingcai Meng
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Stoyko
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Celine Marlin Andrews
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Parthena Konstantinidou
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Pavol Genzor
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy O
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alexandra R Elchert
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leif Benner
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sushil Sobti
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Esther Y Katz
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Astrid D Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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21
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Hughes DC, Hardee JP, Waddell DS, Goodman CA. CORP: Gene delivery into murine skeletal muscle using in vivo electroporation. J Appl Physiol (1985) 2022; 133:41-59. [PMID: 35511722 DOI: 10.1152/japplphysiol.00088.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The strategy of gene delivery into skeletal muscles has provided exciting avenues in identifying new potential therapeutics towards muscular disorders and addressing basic research questions in muscle physiology through overexpression and knockdown studies. In vivo electroporation methodology offers a simple, rapidly effective technique for the delivery of plasmid DNA into post-mitotic skeletal muscle fibers and the ability to easily explore the molecular mechanisms of skeletal muscle plasticity. The purpose of this review is to describe how to robustly electroporate plasmid DNA into different hindlimb muscles of rodent models. Further, key parameters (e.g., voltage, hyaluronidase, plasmid concentration) which contribute to the successful introduction of plasmid DNA into skeletal muscle fibers will be discussed. In addition, details on processing tissue for immunohistochemistry and fiber cross-sectional area (CSA) analysis will be outlined. The overall goal of this review is to provide the basic and necessary information needed for successful implementation of in vivo electroporation of plasmid DNA and thus open new avenues of discovery research in skeletal muscle physiology.
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Affiliation(s)
- David C Hughes
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Justin P Hardee
- Centre for Muscle Research (CMR), Department of Anatomy and Physiology, The University of Melbourne, Victoria, Australia
| | - David S Waddell
- Department of Biology, University of North Florida, Jacksonville, FL, United States
| | - Craig A Goodman
- Centre for Muscle Research (CMR), Department of Anatomy and Physiology, The University of Melbourne, Victoria, Australia
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22
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Murakawa T, Nakamura T, Kawaguchi K, Murayama F, Zhao N, Stasevich TJ, Kimura H, Fujita N. A Drosophila toolkit for HA-tagged proteins unveils a block in autophagy flux in the last instar larval fat body. Development 2022; 149:274775. [DOI: 10.1242/dev.200243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/27/2022] [Indexed: 01/18/2023]
Abstract
ABSTRACT
For in vivo functional analysis of a protein of interest (POI), multiple transgenic strains with a POI that harbors different tags are needed but generation of these strains is still labor-intensive work. To overcome this, we have developed a versatile Drosophila toolkit with a genetically encoded single-chain variable fragment for the HA epitope tag: ‘HA Frankenbody’. This system allows various analyses of HA-tagged POI in live tissues by simply crossing an HA Frankenbody fly with an HA-tagged POI fly. Strikingly, the GFP-mCherry tandem fluorescent-tagged HA Frankenbody revealed a block in autophagic flux and an accumulation of enlarged autolysosomes in the last instar larval and prepupal fat body. Mechanistically, lysosomal activity was downregulated at this stage, and endocytosis, but not autophagy, was indispensable for the swelling of lysosomes. Furthermore, forced activation of lysosomes by fat body-targeted overexpression of Mitf, the single MiTF/TFE family gene in Drosophila, suppressed the lysosomal swelling and resulted in pupal lethality. Collectively, we propose that downregulated lysosomal function in the fat body plays a role in the metamorphosis of Drosophila.
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Affiliation(s)
- Tadayoshi Murakawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tsuyoshi Nakamura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Kohei Kawaguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Futoshi Murayama
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- World Research Hub Initiative, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- World Research Hub Initiative, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Naonobu Fujita
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Precursory Research for Embryonic Science & Technology (PRESTO), Japan Science & Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
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23
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Recent Advancements in Tracking Bacterial Effector Protein Translocation. Microorganisms 2022; 10:microorganisms10020260. [PMID: 35208715 PMCID: PMC8876096 DOI: 10.3390/microorganisms10020260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria-host interactions are characterized by the delivery of bacterial virulence factors, i.e., effectors, into host cells where they counteract host immunity and exploit host responses allowing bacterial survival and spreading. These effectors are translocated into host cells by means of dedicated secretion systems such as the type 3 secretion system (T3SS). A comprehensive understanding of effector translocation in a spatio-temporal manner is of critical importance to gain insights into an effector’s mode of action. Various approaches have been developed to understand timing and order of effector translocation, quantities of translocated effectors and their subcellular localization upon translocation into host cells. Recently, the existing toolset has been expanded by newly developed state-of-the art methods to monitor bacterial effector translocation and dynamics. In this review, we elaborate on reported methods and discuss recent advances and shortcomings in this area of tracking bacterial effector translocation.
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24
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Zou J, Cai Z, Liang Z, Liang Y, Zhang G, Yang J, Zhang Y, Lin H, Tan M. Different fusion tags affect the activity of ubiquitin overexpression on spastin protein stability. Eur J Histochem 2021; 65. [PMID: 34873900 PMCID: PMC8678624 DOI: 10.4081/ejh.2021.3352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/23/2021] [Indexed: 11/23/2022] Open
Abstract
Spastin is one of the proteins which lead to hereditary spastic paraplegia (HSP), whose dysfunction towards microtubule severing and membrane transporting is critically important. The present study is to elucidate the mechanisms of the protein stability regulation of spastin. The ubiquitin encoding plasmids were transfected into COS-7 cells with different fusion tags including Green Fluorescent Protein (GFP), mCherry and Flag. The expression level of spastin was detected, microtubule severing activity and neurite outgrowth were quantified. The data showed that ubiquitin overexpression significantly induced the decreased expression of spastin, suppressed the activity of microtubule severing in COS-7 cells and inhibited the promoting effect on neurite outgrowth in cultured hippocampal neurons. Furthermore, when modulating the overexpression experiments of ubiquitin, it was found that relatively small tag like Flag, but not large tags such as GFP or mCherry fused with ubiquitin, retained the activity on spastin stability. The present study investigated the effects of small/large tags addition to ubiquitin and the novel mechanisms of post-transcriptional modifications of spastin on regulating neurite outgrowth, in the attempt to experimentally elucidate the mechanisms that control the level or stability of spastin in hereditary spastic paraplegia.
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Affiliation(s)
- Jianyu Zou
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Zhenbin Cai
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Zhi Liang
- Department of Orthopaedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen.
| | - Yaozhong Liang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Guowei Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Jie Yang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Yunlong Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Hongsheng Lin
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
| | - Minghui Tan
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou.
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25
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Complexome Profiling: Assembly and Remodeling of Protein Complexes. Int J Mol Sci 2021; 22:ijms22157809. [PMID: 34360575 PMCID: PMC8346016 DOI: 10.3390/ijms22157809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.
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26
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Low TY, Syafruddin SE, Mohtar MA, Vellaichamy A, A Rahman NS, Pung YF, Tan CSH. Recent progress in mass spectrometry-based strategies for elucidating protein-protein interactions. Cell Mol Life Sci 2021; 78:5325-5339. [PMID: 34046695 PMCID: PMC8159249 DOI: 10.1007/s00018-021-03856-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023]
Abstract
Protein-protein interactions are fundamental to various aspects of cell biology with many protein complexes participating in numerous fundamental biological processes such as transcription, translation and cell cycle. MS-based proteomics techniques are routinely applied for characterising the interactome, such as affinity purification coupled to mass spectrometry that has been used to selectively enrich and identify interacting partners of a bait protein. In recent years, many orthogonal MS-based techniques and approaches have surfaced including proximity-dependent labelling of neighbouring proteins, chemical cross-linking of two interacting proteins, as well as inferring PPIs from the co-behaviour of proteins such as the co-fractionating profiles and the thermal solubility profiles of proteins. This review discusses the underlying principles, advantages, limitations and experimental considerations of these emerging techniques. In addition, a brief account on how MS-based techniques are used to investigate the structural and functional properties of protein complexes, including their topology, stoichiometry, copy number and dynamics, are discussed.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia.
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | | | - Nisa Syakila A Rahman
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000, Kuala Lumpur, Malaysia
| | - Yuh-Fen Pung
- Division of Biomedical Science, University of Nottingham Malaysia, 43500, Semenyih, Malaysia
| | - Chris Soon Heng Tan
- Department of Chemistry, College of Science , Southern University of Science and Technology, Shenzhen, 518055, China.
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Wan P, Long E, Li Z, Zhu Y, Su W, Zhuo Y. TET-dependent GDF7 hypomethylation impairs aqueous humor outflow and serves as a potential therapeutic target in glaucoma. Mol Ther 2021; 29:1639-1657. [PMID: 33388417 PMCID: PMC8058441 DOI: 10.1016/j.ymthe.2020.12.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/15/2020] [Accepted: 12/18/2020] [Indexed: 01/03/2023] Open
Abstract
Glaucoma is the leading cause of irreversible vision loss, affecting more than 70 million individuals worldwide. Circulatory disturbances of aqueous humor (AH) have long been central pathological contributors to glaucomatous lesions. Thus, targeting the AH outflow is a promising approach to treat glaucoma. However, the epigenetic mechanisms initiating AH outflow disorders and the targeted treatments remain to be developed. Studying glaucoma patients, we identified GDF7 (growth differentiation factor 7) hypomethylation as a crucial event in the onset of AH outflow disorders. Regarding the underlying mechanism, the hypomethylated GDF7 promoter was responsible for the increased GDF7 production and secretion in primary open-angle glaucoma (POAG). Excessive GDF7 protein promoted trabecular meshwork (TM) fibrosis through bone morphogenetic protein receptor type 2 (BMPR2)/Smad signaling and upregulated pro-fibrotic genes, α-smooth muscle actin (α-SMA) and fibronectin (FN). GDF7 protein expression formed a positive feedback loop in glaucomatous TM (GTM). This positive feedback loop was dependent on the activated TET (ten-eleven translocation) enzyme, which kept the GDF7 promoter region hypomethylated. The phenotypic transition in TM fortified the AH outflow resistance, thus elevating the intraocular pressure (IOP) and attenuating the nerve fiber layer. This methylation-dependent mechanism is also confirmed by a machine-learning model in silico with a specificity of 84.38% and a sensitivity of 89.38%. In rhesus monkeys, we developed GDF7 neutralization therapy to inhibit TM fibrosis and consequent AH outflow resistance that contributes to glaucoma. The neutralization therapy achieved high-efficiency control of the IOP (from 21.3 ± 0.3 to 17.6 ± 0.2 mmHg), a three-fold improvement in the outflow facility (from 0.1 to 0.3 μL/min · mmHg), and protection of nerve fibers. This study provides new insights into the epigenetic mechanism of glaucoma and proposes an innovative GDF7 neutralization therapy as a promising intervention.
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Affiliation(s)
- Peixing Wan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erping Long
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhidong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Yingting Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
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28
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Choquet D, Sainlos M, Sibarita JB. Advanced imaging and labelling methods to decipher brain cell organization and function. Nat Rev Neurosci 2021; 22:237-255. [PMID: 33712727 DOI: 10.1038/s41583-021-00441-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2021] [Indexed: 01/31/2023]
Abstract
The brain is arguably the most complex organ. The branched and extended morphology of nerve cells, their subcellular complexity, the multiplicity of brain cell types as well as their intricate connectivity and the scattering properties of brain tissue present formidable challenges to the understanding of brain function. Neuroscientists have often been at the forefront of technological and methodological developments to overcome these hurdles to visualize, quantify and modify cell and network properties. Over the last few decades, the development of advanced imaging methods has revolutionized our approach to explore the brain. Super-resolution microscopy and tissue imaging approaches have recently exploded. These instrumentation-based innovations have occurred in parallel with the development of new molecular approaches to label protein targets, to evolve new biosensors and to target them to appropriate cell types or subcellular compartments. We review the latest developments for labelling and functionalizing proteins with small localization and functionalized reporters. We present how these molecular tools are combined with the development of a wide variety of imaging methods that break either the diffraction barrier or the tissue penetration depth limits. We put these developments in perspective to emphasize how they will enable step changes in our understanding of the brain.
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Affiliation(s)
- Daniel Choquet
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France. .,University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, Bordeaux, France.
| | - Matthieu Sainlos
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
| | - Jean-Baptiste Sibarita
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
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29
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Bosch JA, Birchak G, Perrimon N. Precise genome engineering in Drosophila using prime editing. Proc Natl Acad Sci U S A 2021; 118:e2021996118. [PMID: 33443210 PMCID: PMC7817132 DOI: 10.1073/pnas.2021996118] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Precise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double-strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organism Drosophila melanogaster and developed conditions for optimal editing. By expressing prime editing components in cultured cells or somatic cells of transgenic flies, we precisely introduce premature stop codons in three classical visible marker genes, ebony, white, and forked Furthermore, by restricting editing to germ cells, we demonstrate efficient germ-line transmission of a precise edit in ebony to 36% of progeny. Our results suggest that prime editing is a useful system in Drosophila to study gene function, such as engineering precise point mutations, deletions, or epitope tags.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
| | - Gabriel Birchak
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
- HHMI, Harvard Medical School, Boston, MA 02115
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30
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Mahmoudi Gomari M, Saraygord-Afshari N, Farsimadan M, Rostami N, Aghamiri S, Farajollahi MM. Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry. Biotechnol Adv 2020; 45:107653. [PMID: 33157154 DOI: 10.1016/j.biotechadv.2020.107653] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 01/16/2023]
Abstract
Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Saraygord-Afshari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran
| | - Shahin Aghamiri
- Student research committee, Department of medical biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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31
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Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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32
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Doh JK, Tobin SJ, Beatty KE. MiniVIPER Is a Peptide Tag for Imaging and Translocating Proteins in Cells. Biochemistry 2020; 59:3051-3059. [PMID: 32786411 DOI: 10.1021/acs.biochem.0c00526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Microscopy allows researchers to interrogate proteins within a cellular context. To deliver protein-specific contrast, we developed a new class of genetically encoded peptide tags called versatile interacting peptide (VIP) tags. VIP tags deliver a reporter to a target protein via the formation of a heterodimer between the peptide tag and an exogenously added probe peptide. We report herein a new VIP tag named MiniVIPER, which is comprised of a MiniE-MiniR heterodimer. We first demonstrated the selectivity of MiniVIPER by labeling three cellular targets: transferrin receptor 1 (TfR1), histone protein H2B, and the mitochondrial protein TOMM20. We showed that either MiniE or MiniR could serve as the genetically encoded tag. Next, we demonstrated MiniVIPER's versatility by generating five spectrally distinct probe peptides to label tagged TfR1 on live cells. Lastly, we demonstrated two new applications for VIP tags. First, we used MiniVIPER in combination with another VIP tag, VIPER, to selectively label two different proteins in a single cell (e.g., TfR1 with H2B or TOMM20). Second, we used MiniVIPER to translocate a fluorescent protein to the nucleus through in situ dimerization of mCherry with H2B-mEmerald. In summary, MiniVIPER is a new peptide tag that enables multitarget imaging and artificial dimerization of proteins in cells.
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Affiliation(s)
- Julia K Doh
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Savannah J Tobin
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Kimberly E Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, United States
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33
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Soliman SHA, Stark AE, Gardner ML, Harshman SW, Breece CC, Amari F, Orlacchio A, Chen M, Tessari A, Martin JA, Visone R, Freitas MA, La Perle KMD, Palmieri D, Coppola V. Tagging enhances histochemical and biochemical detection of Ran Binding Protein 9 in vivo and reveals its interaction with Nucleolin. Sci Rep 2020; 10:7138. [PMID: 32346083 PMCID: PMC7188826 DOI: 10.1038/s41598-020-64047-8] [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: 11/02/2019] [Accepted: 04/08/2020] [Indexed: 12/19/2022] Open
Abstract
The lack of tools to reliably detect RanBP9 in vivo has significantly hampered progress in understanding the biological functions of this scaffold protein. We report here the generation of a novel mouse strain, RanBP9-TT, in which the endogenous protein is fused with a double (V5-HA) epitope tag at the C-terminus. We show that the double tag does not interfere with the essential functions of RanBP9. In contrast to RanBP9 constitutive knock-out animals, RanBP9-TT mice are viable, fertile and do not show any obvious phenotype. The V5-HA tag allows unequivocal detection of RanBP9 both by IHC and WB. Importantly, immunoprecipitation and mass spectrometry analyses reveal that the tagged protein pulls down known interactors of wild type RanBP9. Thanks to the increased detection power, we are also unveiling a previously unknown interaction with Nucleolin, a protein proposed as an ideal target for cancer treatment. In summary, we report the generation of a new mouse line in which RanBP9 expression and interactions can be reliably studied by the use of commercially available αtag antibodies. The use of this line will help to overcome some of the existing limitations in the study of RanBP9 and potentially unveil unknown functions of this protein in vivo such as those linked to Nucleolin.
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Affiliation(s)
- Shimaa H A Soliman
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
- Department of Medicine, Dentistry and Biotechnology, G. d'Annunzio University of Chieti, Chieti, Italy
| | - Aaron E Stark
- Genetically Engineered Mouse Modeling Core, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
| | - Miranda L Gardner
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
| | - Sean W Harshman
- Air Force Research Laboratory, Wright-Patterson AFB, 45433, Ohio, USA
| | - Chelssie C Breece
- Department of Veterinary Biosciences and Comparative Pathology & Mouse Phenotyping Shared Resource, College of Veterinary Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, 43210, Ohio, USA
| | - Foued Amari
- Genetically Engineered Mouse Modeling Core, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
| | - Arturo Orlacchio
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
| | - Min Chen
- Genetically Engineered Mouse Modeling Core, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
| | - Anna Tessari
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
| | - Jennifer A Martin
- Air Force Research Laboratory, Wright-Patterson AFB, 45433, Ohio, USA
| | - Rosa Visone
- Department of Medicine, Dentistry and Biotechnology, G. d'Annunzio University of Chieti, Chieti, Italy
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
| | - Krista M D La Perle
- Department of Veterinary Biosciences and Comparative Pathology & Mouse Phenotyping Shared Resource, College of Veterinary Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, 43210, Ohio, USA
| | - Dario Palmieri
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA.
- Genetically Engineered Mouse Modeling Core, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, USA.
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34
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Shirzadeh M, Poltash ML, Laganowsky A, Russell DH. Structural Analysis of the Effect of a Dual-FLAG Tag on Transthyretin. Biochemistry 2020; 59:1013-1022. [PMID: 32101399 PMCID: PMC7171973 DOI: 10.1021/acs.biochem.0c00105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recombinant proteins have increased our knowledge regarding the physiological role of proteins; however, affinity purification tags are often not cleaved prior to analysis, and their effects on protein structure, stability and assembly are often overlooked. In this study, the stabilizing effects of an N-terminus dual-FLAG (FT2) tag fusion to transthyretin (TTR), a construct used in previous studies, are investigated using native ion mobility-mass spectrometry (IM-MS). A combination of collision-induced unfolding and variable-temperature electrospray ionization is used to compare gas- and solution-phase stabilities of FT2-TTR to wild-type and C-terminal tagged TTR. Despite an increased stability of both gas- and solution-phase FT2-TTR, thermal degradation of FT2-TTR was observed at elevated temperatures, viz., backbone cleavage occurring between Lys9 and Cys10. This cleavage reaction is consistent with previously reported metalloprotease activity of TTR [Liz et al. 2009] and is suppressed by either metal chelation or excess zinc. This study brings to the fore the effect of affinity tag stabilization of TTR and emphasizes unprecedented detail afforded by native IM-MS to assess structural discrepancies of recombinant proteins from their wild-type counterparts.
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Affiliation(s)
- Mehdi Shirzadeh
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Michael L Poltash
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
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35
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Controlling cell-to-cell variability with synthetic gene circuits. Biochem Soc Trans 2019; 47:1795-1804. [DOI: 10.1042/bst20190295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 02/05/2023]
Abstract
Cell-to-cell variability originating, for example, from the intrinsic stochasticity of gene expression, presents challenges for designing synthetic gene circuits that perform robustly. Conversely, synthetic biology approaches are instrumental in uncovering mechanisms underlying variability in natural systems. With a focus on reducing noise in individual genes, the field has established a broad synthetic toolset. This includes noise control by engineering of transcription and translation mechanisms either individually, or in combination to achieve independent regulation of mean expression and its variability. Synthetic feedback circuits use these components to establish more robust operation in closed-loop, either by drawing on, but also by extending traditional engineering concepts. In this perspective, we argue that major conceptual advances will require new theory of control adapted to biology, extensions from single genes to networks, more systematic considerations of origins of variability other than intrinsic noise, and an exploration of how noise shaping, instead of noise reduction, could establish new synthetic functions or help understanding natural functions.
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36
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Doh JK, Enns CA, Beatty KE. Implementing VIPER for Imaging Cellular Proteins by Fluorescence Microscopy. Bio Protoc 2019; 9:e3413. [PMID: 32665966 PMCID: PMC7360171 DOI: 10.21769/bioprotoc.3413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
Genetically-encoded tags are useful tools for multicolor and multi-scale cellular imaging. Versatile Interacting Peptide (VIP) tags, such as VIPER, are new genetically-encoded tags that can be used in various imaging applications. VIP tags consist of a coiled-coil heterodimer, with one peptide serving as the genetic tag and the other ("probe peptide") delivering a reporter compatible with imaging. Heterodimer formation is rapid and specific, allowing proteins to be selectively labeled for live-cell and fixed-cell imaging. In this Bio-Protocol, we include a detailed guide for implementing the VIPER technology for imaging receptors on live cells and intracellular targets in fixed cells. This protocol is complemented by two other Bio-Protocols outlining the use of VIPER (Doh et al., 2019a and 2019b).
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Affiliation(s)
- Julia K. Doh
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Caroline A. Enns
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Kimberly E. Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, USA
- OHSU Center for Spatial Systems Biomedicine, Oregon Health & Science University, Portland, Oregon 97239, USA
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Stevens LM, Zhang Y, Volnov Y, Chen G, Stein DS. Isolation of secreted proteins from Drosophila ovaries and embryos through in vivo BirA-mediated biotinylation. PLoS One 2019; 14:e0219878. [PMID: 31658274 PMCID: PMC6816556 DOI: 10.1371/journal.pone.0219878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
The extraordinarily strong non-covalent interaction between biotin and avidin (kD = 10-14-10-16) has permitted this interaction to be used in a wide variety of experimental contexts. The Biotin Acceptor Peptide (BAP), a 15 amino acid motif that can be biotinylated by the E. coli BirA protein, has been fused to proteins-of-interest, making them substrates for in vivo biotinylation. Here we report on the construction and characterization of a modified BirA bearing signals for secretion and endoplasmic reticulum (ER) retention, for use in experimental contexts requiring biotinylation of secreted proteins. When expressed in the Drosophila female germline or ovarian follicle cells under Gal4-mediated transcriptional control, the modified BirA protein could be detected and shown to be enzymatically active in ovaries and progeny embryos. Surprisingly, however, it was not efficiently retained in the ER, and instead appeared to be secreted. To determine whether this secreted protein, now designated secBirA, could biotinylate secreted proteins, we generated BAP-tagged versions of two secreted Drosophila proteins, Torsolike (Tsl) and Gastrulation Defective (GD), which are normally expressed maternally and participate in embryonic pattern formation. Both Tsl-BAP and GD-BAP were shown to exhibit normal patterning activity. Co-expression of Tsl-BAP together with secBirA in ovarian follicle cells resulted in its biotinylation, which permitted its isolation from both ovaries and progeny embryos using Avidin-coupled affinity matrix. In contrast, co-expression with secBirA in the female germline did not result in detectable biotinylation of GD-BAP, possibly because the C-terminal location of the BAP tag made it inaccessible to BirA in vivo. Our results indicate that secBirA directs biotinylation of proteins bound for secretion in vivo, providing access to powerful experimental approaches for secreted proteins-of-interest. However, efficient biotinylation of target proteins may vary depending upon the location of the BAP tag or other structural features of the protein.
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Affiliation(s)
- Leslie M. Stevens
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Yuan Zhang
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Yuri Volnov
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Geng Chen
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - David S. Stein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
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Rosano GL, Morales ES, Ceccarelli EA. New tools for recombinant protein production in Escherichia coli: A 5-year update. Protein Sci 2019; 28:1412-1422. [PMID: 31219641 PMCID: PMC6635841 DOI: 10.1002/pro.3668] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 06/10/2019] [Indexed: 12/11/2022]
Abstract
The production of proteins in sufficient amounts is key for their study or use as biotherapeutic agents. Escherichia coli is the host of choice for recombinant protein production given its fast growth, easy manipulation, and cost-effectiveness. As such, its protein production capabilities are continuously being improved. Also, the associated tools (such as plasmids and cultivation conditions) are subject of ongoing research to optimize product yield. In this work, we review the latest advances in recombinant protein production in E. coli.
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Affiliation(s)
- Germán L. Rosano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
| | - Enrique S. Morales
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
| | - Eduardo A. Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET. Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
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