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Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, Turan D, Hulstaert N, Eeckhaut H, Vandermarliere E, Martens L, Degroeve S, De Neve W, Vranken W, Callewaert N. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nat Commun 2021; 12:6414. [PMID: 34741024 PMCID: PMC8571348 DOI: 10.1038/s41467-021-26720-y] [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: 11/25/2020] [Accepted: 10/15/2021] [Indexed: 11/09/2022] Open
Abstract
While transcriptome- and proteome-wide technologies to assess processes in protein biogenesis are now widely available, we still lack global approaches to assay post-ribosomal biogenesis events, in particular those occurring in the eukaryotic secretory system. We here develop a method, SECRiFY, to simultaneously assess the secretability of >105 protein fragments by two yeast species, S. cerevisiae and P. pastoris, using custom fragment libraries, surface display and a sequencing-based readout. Screening human proteome fragments with a median size of 50-100 amino acids, we generate datasets that enable datamining into protein features underlying secretability, revealing a striking role for intrinsic disorder and chain flexibility. The SECRiFY methodology generates sufficient amounts of annotated data for advanced machine learning methods to deduce secretability patterns. The finding that secretability is indeed a learnable feature of protein sequences provides a solid base for application-focused studies.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium. .,Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium. .,Department of Biochemistry and Biophysics, UCSF, San Francisco, CA, USA.
| | - Pathmanaban Ramasamy
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium ,grid.8767.e0000 0001 2290 8069Structural Biology Brussels, VUB, Brussels, Belgium ,grid.11486.3a0000000104788040Structural Biology Research Center, VIB, Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels (IB)2, ULB-VUB, Brussels, Belgium
| | - Jasper Zuallaert
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium ,grid.510328.dCenter for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon, South Korea ,grid.5342.00000 0001 2069 7798IDLab, ELIS, UGent, Ghent, Belgium
| | - Robbin Bouwmeester
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Berre Van Moer
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Davy Maddelein
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Demet Turan
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Niels Hulstaert
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hannah Eeckhaut
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Elien Vandermarliere
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Lennart Martens
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sven Degroeve
- grid.11486.3a0000000104788040Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium ,grid.5342.00000 0001 2069 7798Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Wesley De Neve
- grid.510328.dCenter for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon, South Korea ,grid.5342.00000 0001 2069 7798IDLab, ELIS, UGent, Ghent, Belgium
| | - Wim Vranken
- grid.8767.e0000 0001 2290 8069Structural Biology Brussels, VUB, Brussels, Belgium ,grid.11486.3a0000000104788040Structural Biology Research Center, VIB, Brussels, Belgium ,Interuniversity Institute of Bioinformatics in Brussels (IB)2, ULB-VUB, Brussels, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde, Belgium. .,Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium.
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Boone M, De Koker A, Callewaert N. Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction. Nucleic Acids Res 2018; 46:2701-2721. [PMID: 29514322 PMCID: PMC5888575 DOI: 10.1093/nar/gky167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/05/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022] Open
Abstract
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application.
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Affiliation(s)
- Morgane Boone
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
| | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Zwijnaarde 9052, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium
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3
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Comprehensive Analysis and Characterization of Linear Antigenic Domains on HN Protein from Genotype VII Newcastle Disease Virus Using Yeast Surface Display System. PLoS One 2015; 10:e0131723. [PMID: 26121247 PMCID: PMC4488241 DOI: 10.1371/journal.pone.0131723] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/04/2015] [Indexed: 11/19/2022] Open
Abstract
Circulation of genotype VII Newcastle disease virus (NDV) has posed a great threat for the poultry industry worldwide. Antibodies against Hemagglutinin-neuraminidase (HN), a membrane protein of NDV with critical roles in NDV infection, have been reported to provide chickens protection from NDV infection. In this study, we comprehensively analyzed the in vivo antibody responses against the linear antigenic domains of the HN protein from genotype VII NDV using a yeast surface display system. The results revealed four distinct regions of HN, P1 (1-52aa), P2 (53-192aa), P3 (193-302aa) and P4 (303-571aa), respectively, according to their antigenic potency. Analysis by FACS and ELISA assay indicated P2 to be the dominant linear antigenic domain, with the immunogenic potency to protect the majority of chickens from NDV challenge. In contrast, the P1, P3 and P4 domains showed weak antigenicity in vivo and could not protect chickens from NDV challenge. These results provide important insight into the characteristic of humoral immune responses elicited by HN of NDV in vivo.
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4
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Bulloch EM, Kingston RL. Identifying protein domains by global analysis of soluble fragment data. Anal Biochem 2014; 465:53-62. [DOI: 10.1016/j.ab.2014.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/17/2014] [Accepted: 06/25/2014] [Indexed: 01/11/2023]
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5
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Moser S, Johnsson K. Yeast Three-Hybrid Screening for Identifying Anti-Tuberculosis Drug Targets. Chembiochem 2013; 14:2239-42. [DOI: 10.1002/cbic.201300472] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Indexed: 01/03/2023]
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6
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Sun J, Yan Y, Sun S, Shu X, Zhu C, Zhu J. DNA binding and reactivity assays based on in-frame protein expression. Chem Sci 2013. [DOI: 10.1039/c2sc21464d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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ORF-selector ESPRIT: A second generation library screen for soluble protein expression employing precise open reading frame selection. J Struct Biol 2011; 175:189-97. [DOI: 10.1016/j.jsb.2011.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 04/09/2011] [Accepted: 04/10/2011] [Indexed: 12/24/2022]
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8
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Pedelacq JD, Nguyen HB, Cabantous S, Mark BL, Listwan P, Bell C, Friedland N, Lockard M, Faille A, Mourey L, Terwilliger TC, Waldo GS. Experimental mapping of soluble protein domains using a hierarchical approach. Nucleic Acids Res 2011; 39:e125. [PMID: 21771856 PMCID: PMC3185438 DOI: 10.1093/nar/gkr548] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Exploring the function and 3D space of large multidomain protein targets often requires sophisticated experimentation to obtain the targets in a form suitable for structure determination. Screening methods capable of selecting well-expressed, soluble fragments from DNA libraries exist, but require the use of automation to maximize chances of picking a few good candidates. Here, we describe the use of an insertion dihydrofolate reductase (DHFR) vector to select in-frame fragments and a split-GFP assay technology to filter-out constructs that express insoluble protein fragments. With the incorporation of an IPCR step to create high density, focused sublibraries of fragments, this cost-effective method can be performed manually with no a priori knowledge of domain boundaries while permitting single amino acid resolution boundary mapping. We used it on the well-characterized p85α subunit of the phosphoinositide-3-kinase to demonstrate the robustness and efficiency of our methodology. We then successfully tested it onto the polyketide synthase PpsC from Mycobacterium tuberculosis, a potential drug target involved in the biosynthesis of complex lipids in the cell envelope. X-ray quality crystals from the acyl-transferase (AT), dehydratase (DH) and enoyl-reductase (ER) domains have been obtained.
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Affiliation(s)
- Jean-Denis Pedelacq
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse, France.
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9
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Xu W, Han L, Lin Z. Screening of random peptide library of hemagglutinin from pandemic 2009 A(H1N1) influenza virus reveals unexpected antigenically important regions. PLoS One 2011; 6:e18016. [PMID: 21437206 PMCID: PMC3060926 DOI: 10.1371/journal.pone.0018016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 02/18/2011] [Indexed: 11/19/2022] Open
Abstract
The antigenic structure of the membrane protein hemagglutinin (HA) from the 2009 A(H1N1) influenza virus was dissected with a high-throughput screening method using complex antisera. The approach involves generating yeast cell libraries displaying a pool of random peptides of controllable lengths on the cell surface, followed by one round of fluorescence-activated cell sorting (FACS) against antisera from mouse, goat and human, respectively. The amino acid residue frequency appearing in the antigenic peptides at both the primary sequence and structural level was determined and used to identify "hot spots" or antigenically important regions. Unexpectedly, different antigenic structures were seen for different antisera. Moreover, five antigenic regions were identified, of which all but one are located in the conserved HA stem region that is responsible for membrane fusion. Our findings are corroborated by several recent studies on cross-neutralizing H1 subtype antibodies that recognize the HA stem region. The antigenic peptides identified may provide clues for creating peptide vaccines with better accessibility to memory B cells and better induction of cross-neutralizing antibodies than the whole HA protein. The scheme used in this study enables a direct mapping of the antigenic regions of viral proteins recognized by antisera, and may be useful for dissecting the antigenic structures of other viral proteins.
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Affiliation(s)
- Wanghui Xu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Lu Han
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University, Beijing, China
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10
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A combinatorial method to enable detailed investigation of protein–protein interactions. Future Med Chem 2011; 3:271-82. [DOI: 10.4155/fmc.10.289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Successful structural investigations of protein–protein interactions can be facilitated by studying only the core interacting regions of the constituent proteins. However, attempting the discovery of stable core complexes using informed trial-and-error approaches can prove time and resource intensive. Methods: We describe a valuable extension of combinatorial domain hunting (CDH), a technology for the timely elucidation of soluble protein truncations. The new method, CDH2, enables empirical discovery of stable protein–protein core complexes. CDH2 is demonstrated ab initio using a previously well-characterized Hsp90/Cdc37 complex. Results: Without using a priori information, we demonstrate the isolation of stable protein–protein complexes, suitable for further analyses. Discussion: This resource-efficient process can provide protein complexes for screening of compounds designed to modulate protein–protein interactions, thus facilitating novel drug discovery.
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An Y, Meresse P, Mas PJ, Hart DJ. CoESPRIT: a library-based construct screening method for identification and expression of soluble protein complexes. PLoS One 2011; 6:e16261. [PMID: 21364980 PMCID: PMC3043051 DOI: 10.1371/journal.pone.0016261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Accepted: 12/13/2010] [Indexed: 11/29/2022] Open
Abstract
Structural and biophysical studies of protein complexes require multi-milligram quantities of soluble material. Subunits are often unstable when expressed separately so co-expression strategies are commonly employed since in vivo complex formation can provide stabilising effects. Defining constructs for subunit co-expression experiments is difficult if the proteins are poorly understood. Even more problematic is when subunit polypeptide chains co-fold since individually they do not have predictable domains. We have developed CoESPRIT, a modified version of the ESPRIT random library construct screen used previously on single proteins, to express soluble protein complexes. A random library of target constructs is screened against a fixed bait protein to identify stable complexes. In a proof-of-principle study, C-terminal fragments of the influenza polymerase PB2 subunit containing folded domains were isolated using importin alpha as bait. Separately, a C-terminal fragment of the PB1 subunit was used as bait to trap N-terminal fragments of PB2 resulting in co-folded complexes. Subsequent expression of the target protein without the bait indicates whether the target is independently stable, or co-folds with its partner. This highly automated method provides an efficient strategy for obtaining recombinant protein complexes at yields compatible with structural, biophysical and functional studies.
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Affiliation(s)
- Yingfeng An
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Patrick Meresse
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Philippe J. Mas
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
| | - Darren J. Hart
- Grenoble Outstation, European Molecular Biology Laboratory, BP181, Grenoble, France
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI3265, Grenoble, France
- * E-mail:
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12
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Rawlings AE, Levdikov VM, Blagova E, Colledge VL, Mas PJ, Tunaley J, Vavrova L, Wilson KS, Barak I, Hart DJ, Wilkinson AJ. Expression of soluble, active fragments of the morphogenetic protein SpoIIE from Bacillus subtilis using a library-based construct screen. Protein Eng Des Sel 2010; 23:817-25. [PMID: 20817757 PMCID: PMC2953957 DOI: 10.1093/protein/gzq057] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SpoIIE is a dual function protein that plays important roles during sporulation in Bacillus subtilis. It binds to the tubulin-like protein FtsZ causing the cell division septum to relocate from mid-cell to the cell pole, and it dephosphorylates SpoIIAA phosphate leading to establishment of differential gene expression in the two compartments following the asymmetric septation. Its 872 residue polypeptide contains a multiple-membrane spanning sequence at the N-terminus and a PP2C phosphatase domain at the C-terminus. The central segment that binds to FtsZ is unlike domains of known structure or function, moreover the domain boundaries are poorly defined and this has hampered the expression of soluble fragments of SpoIIE at the levels required for structural studies. Here we have screened over 9000 genetic constructs of spoIIE using a random incremental truncation library approach, ESPRIT, to identify a number of soluble C-terminal fragments of SpoIIE that were aligned with the protein sequence to map putative domains and domain boundaries. The expression and purification of three fragments were optimised, yielding multimilligram quantities of the PP2C phosphatase domain, the putative FtsZ-binding domain and a larger fragment encompassing both these domains. All three fragments are monomeric and the PP2C domain-containing fragments have phosphatase activity.
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Affiliation(s)
- Andrea E Rawlings
- Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
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13
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Selection of soluble protein expression constructs: the experimental determination of protein domain boundaries. Biochem Soc Trans 2010; 38:908-13. [DOI: 10.1042/bst0380908] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Proteins can contain multiple domains each of which is capable of possessing a separate independent function and three-dimensional structure. It is often useful to clone and express individual protein domains to study their biochemical properties and for structure determination. However, the annotated domain boundaries in databases such as Pfam or SMART are not always accurate. The present review summarizes various strategies for the experimental determination of protein domain boundaries.
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14
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Yumerefendi H, Tarendeau F, Mas PJ, Hart DJ. ESPRIT: an automated, library-based method for mapping and soluble expression of protein domains from challenging targets. J Struct Biol 2010; 172:66-74. [PMID: 20206698 DOI: 10.1016/j.jsb.2010.02.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 02/24/2010] [Accepted: 02/28/2010] [Indexed: 01/28/2023]
Abstract
Expression of sufficient quantities of soluble protein for structural biology and other applications is often a very difficult task, especially when multimilligram quantities are required. In order to improve yield, solubility or crystallisability of a protein, it is common to subclone shorter genetic constructs corresponding to single- or multi-domain fragments. However, it is not always clear where domain boundaries are located, especially when working on novel targets with little or no sequence similarity to other proteins. Several methods have been described employing aspects of directed evolution to the recombinant expression of challenging proteins. These combine the construction of a random library of genetic constructs of a target with a screening or selection process to identify solubly expressing protein fragments. Here we review several datasets from the ESPRIT (Expression of Soluble Proteins by Random Incremental Truncation) technology to provide a view on its capabilities. Firstly, we demonstrate how it functions using the well-characterised NF-kappaB p50 transcription factor as a model system. Secondly, application of ESPRIT to the challenging PB2 subunit of influenza polymerase has led to several novel atomic resolution structures; here we present an overview of the screening phase of that project. Thirdly, analysis of the human kinase TBK1 is presented to show how the ESPRIT technology rapidly addresses the compatibility of challenging targets with the Escherichia coli expression system.
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Affiliation(s)
- Hayretin Yumerefendi
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, Grenoble Cedex 9, France
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15
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Guerriero G, Martin N, Golovko A, Sundström JF, Rask L, Ezcurra I. The RY/Sph element mediates transcriptional repression of maturation genes from late maturation to early seedling growth. THE NEW PHYTOLOGIST 2009; 184:552-565. [PMID: 19659659 DOI: 10.1111/j.1469-8137.2009.02977.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In orthodox seeds, the transcriptional activator ABI3 regulates two major stages in embryo maturation: a mid-maturation (MAT) stage leading to accumulation of storage compounds, and a late maturation (LEA) stage leading to quiescence and desiccation tolerance. Our aim was to elucidate mechanisms for transcriptional shutdown of MAT genes during late maturation, to better understand phase transition between MAT and LEA stages. Using transgenic and transient approaches in Nicotiana, we examined activities of two ABI3-dependent reporter genes driven by multimeric RY and abscisic acid response elements (ABREs) from a Brassica napus napin gene, termed RY and ABRE, where the RY reporter requires ABI3 DNA binding. Expression of RY peaks during mid-maturation and drops during late maturation, mimicking the MAT gene program, and in Arabidopsis thaliana RY elements are over-represented in MAT, but not in LEA, genes. The ABI3 transactivation of RY is inhibited by staurosporine, by a PP2C phosphatase, and by a repressor of maturation genes, VAL1/HSI2. The RY element mediates repression of MAT genes, and we propose that transcriptional shutdown of the MAT program during late maturation involves inhibition of ABI3 DNA binding by dephosphorylation. Later, during seedling growth, VAL1/HSI2 family repressors silence MAT genes by binding RY elements.
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Affiliation(s)
- Gea Guerriero
- KTH Biotechnology, Swedish Center of Biomimetic Fiber Engineering, AlbaNova, SE-106 91, Stockholm, Sweden
| | - Nathalie Martin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23, Uppsala; Sweden
| | - Anna Golovko
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23, Uppsala; Sweden
| | - Jens F Sundström
- Department of Plant Biology and Forest Genetics, SLU, Box 7080, SE-750 07, Uppsala, Sweden
| | - Lars Rask
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23, Uppsala; Sweden
| | - Ines Ezcurra
- KTH Biotechnology, Swedish Center of Biomimetic Fiber Engineering, AlbaNova, SE-106 91, Stockholm, Sweden
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16
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Chen Y, Li S, Chen T, Hua H, Lin Z. Random dissection to select for protein split sites and its application in protein fragment complementation. Protein Sci 2009; 18:399-409. [PMID: 19165722 PMCID: PMC2708047 DOI: 10.1002/pro.42] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 10/23/2008] [Accepted: 11/25/2008] [Indexed: 11/11/2022]
Abstract
To identify protein split sites quickly, a selection procedure by using chloramphenicol acetyl transferase (CAT) as reporter was introduced to search for folded protein fragments from libraries generated by random digestion and reassembly of the target gene, which yielded an abundant amount of DNA fragments with controllable lengths. Experimental results of tryptophan synthase alpha subunit (TSalpha) and TEM-1 beta-lactamase agreed well with what the literature has reported. The solubility of these fragments correlated roughly with the minimum inhibitory concentrations of the CAT fusions. The application of this dissection protocol to protein fragment complementation assay (PCA) was evaluated using aminoglycoside-3'-phosphotransferase I (APH(3')-I) as a model protein. Three nearly bisectional sites and a number of possible split points were identified, and guided by this result, four novel pairs of fragments were tested for complementation. Three out of four pairs partially restored the APH activity with the help of leucine zippers, and a truncated but active APH(3')-I (Delta1-25) was also found. Finally, the weakly active APH(3')-I-(1-253)NZ/CZ (254-271) containing a short 18 residue tag was further improved by error-prone PCR, and a best mutant was obtained showing a fourfold improvement after just one round of evolution. These results demonstrate that protein random dissection based on the CAT selection can provide an efficient search for protein breakage points and guide the design of fragments for protein complementation assay. Furthermore, more active fragment pairs can be achieved with the classical directed evolution approach.
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Affiliation(s)
| | | | | | | | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University1 Tsinghua Garden Road, Beijing 100084, China
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17
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Dyson MR, Perera RL, Shadbolt SP, Biderman L, Bromek K, Murzina NV, McCafferty J. Identification of soluble protein fragments by gene fragmentation and genetic selection. Nucleic Acids Res 2008; 36:e51. [PMID: 18420658 PMCID: PMC2396403 DOI: 10.1093/nar/gkn151] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We describe a new method, which identifies protein fragments for soluble expression in Escherichia coli from a randomly fragmented gene library. Inhibition of E. coli dihydrofolate reductase (DHFR) by trimethoprim (TMP) prevents growth, but this can be relieved by murine DHFR (mDHFR). Bacterial strains expressing mDHFR fusions with the soluble proteins green fluroscent protein (GFP) or EphB2 (SAM domain) displayed markedly increased growth rates with TMP compared to strains expressing insoluble EphB2 (TK domain) or ketosteroid isomerase (KSI). Therefore, mDHFR is affected by the solubility of fusion partners and can act as a reporter of soluble protein expression. Random fragment libraries of the transcription factor Fli1 were generated by deoxyuridine incorporation and endonuclease V cleavage. The fragments were cloned upstream of mDHFR and TMP resistant clones expressing soluble protein were identified. These were found to cluster around the DNA binding ETS domain. A selected Fli1 fragment was expressed independently of mDHFR and was judged to be correctly folded by various biophysical methods including NMR. Soluble fragments of the cell-surface receptor Pecam1 were also identified. This genetic selection method was shown to generate expression clones useful for both structural studies and antibody generation and does not require a priori knowledge of domain architecture.
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Affiliation(s)
- Michael R Dyson
- Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK.
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Savva R, Prodromou C, Driscoll PC. DNA fragmentation based combinatorial approaches to soluble protein expression. Drug Discov Today 2007; 12:939-47. [DOI: 10.1016/j.drudis.2007.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 08/21/2007] [Accepted: 08/28/2007] [Indexed: 11/26/2022]
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