1
|
Rial SA, You Z, Vivoli A, Sean D, Al-Khoury A, Lavoie G, Civelek M, Martinez-Sanchez A, Roux PP, Durcan TM, Lim GE. 14-3-3ζ regulates adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585495. [PMID: 38562727 PMCID: PMC10983991 DOI: 10.1101/2024.03.18.585495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
We previously established the scaffold protein 14-3-3ζ as a critical regulator of adipogenesis and adiposity, but the temporal specificity of its action during adipocyte differentiation remains unclear. To decipher if 14-3-3ζ exerts its regulatory functions on mature adipocytes or on adipose precursor cells (APCs), we generated Adipoq14-3-3ζKO and Pdgfra14-3-3ζKO mouse models. Our findings revealed a pivotal role for 14-3-3ζ in APC differentiation in a sex-dependent manner, whereby male and female Pdgfra14-3-3ζKO mice display impaired or potentiated weight gain, respectively, as well as fat mass. To better understand how 14-3-3ζ regulates the adipogenic transcriptional program in APCs, CRISPR-Cas9 was used to generate TAP-tagged 14-3-3ζ-expressing 3T3-L1 preadipocytes. Using these cells, we examined if the 14-3-3ζ nuclear interactome is enriched with adipogenic regulators during differentiation. Regulators of chromatin remodeling, such as DNMT1 and HDAC1, were enriched in the nuclear interactome of 14-3-3ζ, and their activities were impacted upon 14-3-3ζ depletion. The interactions between 14-3-3ζ and chromatin-modifying enzymes suggested that 14-3-3ζ may control chromatin remodeling during adipogenesis, and this was confirmed by ATAC-seq, which revealed that 14-3-3ζ depletion impacted the accessibility of up to 1,244 chromatin regions corresponding in part to adipogenic genes, promoters, and enhancers during the initial stages of adipogenesis. Moreover, 14-3-3ζ-dependent chromatin accessibility was found to directly correlate with the expression of key adipogenic genes. Altogether, our study establishes 14-3-3ζ as a crucial epigenetic regulator of adipogenesis and highlights the usefulness of deciphering the nuclear 14-3-3ζ interactome to identify novel pro-adipogenic factors and pathways.
Collapse
Affiliation(s)
- SA Rial
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Z You
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC, H3A 2B4, Canada
| | - A Vivoli
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - D Sean
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Amal Al-Khoury
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - G Lavoie
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - M Civelek
- Department of Biomedical Engineering, University of Virginia, Charlottesville, United States
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908
| | - A Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, London, UK
| | - Roux PP
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Québec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - TM Durcan
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC, H3A 2B4, Canada
| | - GE Lim
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| |
Collapse
|
2
|
Ino Y, Yamaoka Y, Tanaka K, Miyakawa K, Nishi M, Hatayama Y, Kimura H, Kimura Y, Ryo A. Integrated tandem affinity protein purification using the polyhistidine plus extra 4 amino acids (HiP4) tag system. Proteomics 2023; 23:e2200334. [PMID: 36807525 DOI: 10.1002/pmic.202200334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
Peptide tag systems are a robust biophysical and biochemical method that is widely used for protein detection and purification. Here, we developed a novel tag system termed "HiP4" (histidine plus four amino acids) whose epitope sequence comprises only seven amino acids (HHHDYDI) that partially overlap with the conventional 6x histidine tag (6xHis-tag). We produced a monoclonal antibody against the HiP4 tag that can be used in multiple immunoassays with high specificity and affinity. Using this system, we developed a tandem affinity purification (TAP) and mass spectrometry (TAP-MS) system for comprehensive protein interactome analysis. The integrated use of nickel bead purification followed by HiP4 tag immunoprecipitation made it possible to reduce nonspecific binding and improve selectivity, leading to the recovery of previously unrecognized proteins that interact with hepatitis B virus X (HBx) protein or TAR DNA-binding protein 43 (TARDBP or TDP-43). Our results indicate that this system may be viable as a simple and powerful tool for TAP-MS that can achieve low background and high selectivity in comprehensive protein-protein interaction analyses.
Collapse
Affiliation(s)
- Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan.,Department of Health Science, Gunma Paz University Graduate School of Health Sciences, Takasaki, Gunma, Japan
| | - Yutaro Yamaoka
- Life Science Laboratory, Technology and Development Division, Kanto Chemical Co. Inc., Isehara, Kanagawa, Japan.,Department of Microbiology, School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Kiho Tanaka
- Department of Microbiology, School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Kei Miyakawa
- Department of Microbiology, School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan.,Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mayuko Nishi
- Department of Microbiology, School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Yasuyoshi Hatayama
- Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan.,Department of Microbiology, School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, Takasaki, Gunma, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan.,Department of Microbiology, School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan.,Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
3
|
A Novel Tandem-Tag Purification Strategy for Challenging Disordered Proteins. Biomolecules 2022; 12:biom12111566. [DOI: 10.3390/biom12111566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) lack well-defined 3D structures and can only be described as ensembles of different conformations. This high degree of flexibility allows them to interact promiscuously and makes them capable of fulfilling unique and versatile regulatory roles in cellular processes. These functional benefits make IDPs widespread in nature, existing in every living organism from bacteria and fungi to plants and animals. Due to their open and exposed structural state, IDPs are much more prone to proteolytic degradation than their globular counterparts. Therefore, the purification of recombinant IDPs requires extra care and caution, such as maintaining low temperature throughout the purification, the use of protease inhibitor cocktails and fast workflow. Even so, in the case of long IDP targets, the appearance of truncated by-products often seems unavoidable. The separation of these unwanted proteins can be very challenging due to their similarity to the parent target protein. Here, we describe a tandem-tag purification method that offers a remedy to this problem. It contains only common affinity-chromatography steps (HisTrap and Heparin) to ensure low cost, easy access and scaling-up for possible industrial use. The effectiveness of the method is demonstrated with four examples, Tau-441 and two of its fragments and the transactivation domain (AF1) of androgen receptor.
Collapse
|
4
|
Vetyskova V, Zouharova M, Bousova K. Production of recombinant human ameloblastin by a fully native purification pathway. Protein Expr Purif 2022; 198:106133. [PMID: 35750297 DOI: 10.1016/j.pep.2022.106133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 12/29/2022]
Abstract
Ameloblastin (Ambn) is an intrinsically disordered protein (IDP) with a specific function of forming heterogenous homooligomers. The oligomeric function is led through a specific sequence encoded by exon 5 of Ambn. Due to the IDP character of Ambn to form oligomers, protein purification is subject to many challenges. Human ameloblastin (AMBN) and its two isoforms, I and II have already been purified as a recombinant protein in a bacterial expression system and functionally characterized in vitro. However, here we present a new purification protocol for the production of native AMBN in its original formation as a homooligomeric heterogeneous IDP. The purification process consists of three chromatographic steps utilizing His-tag and Twin Strep-tag affinity chromatography, along with size exclusion and reverse affinity chromatography. The presented workflow offers the production of AMBN in sufficient yield for in vitro protein characterizations and can be used to produce both AMBN isoforms I and II.
Collapse
Affiliation(s)
- V Vetyskova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 2, 16000, Prague, Czech Republic; Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - M Zouharova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 2, 16000, Prague, Czech Republic; Second Faculty of Medicine, Charles University, 150 06, Prague 5, V Uvalu 84, Czech Republic
| | - K Bousova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 2, 16000, Prague, Czech Republic.
| |
Collapse
|
5
|
Wang S, Wu R, Lu J, Jiang Y, Huang T, Cai YD. Protein-protein interaction networks as miners of biological discovery. Proteomics 2022; 22:e2100190. [PMID: 35567424 DOI: 10.1002/pmic.202100190] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/12/2022]
Abstract
Protein-protein interactions (PPIs) form the basis of a myriad of biological pathways and mechanism, such as the formation of protein-complexes or the components of signaling cascades. Here, we reviewed experimental methods for identifying PPI pairs, including yeast two-hybrid, mass spectrometry, co-localization, and co-immunoprecipitation. Furthermore, a range of computational methods leveraging biochemical properties, evolution history, protein structures and more have enabled identification of additional PPIs. Given the wealth of known PPIs, we reviewed important network methods to construct and analyze networks of PPIs. These methods aid biological discovery through identifying hub genes and dynamic changes in the network, and have been thoroughly applied in various fields of biological research. Lastly, we discussed the challenges and future direction of research utilizing the power of PPI networks. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Steven Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Runxin Wu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jiaqi Lu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Yijia Jiang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tao Huang
- Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
| |
Collapse
|
6
|
Giakomidi D, Bird MF, Guerrini R, Calo G, Lambert DG. Fluorescent opioid receptor ligands as tools to study opioid receptor function. J Pharmacol Toxicol Methods 2021; 113:107132. [PMID: 34728348 DOI: 10.1016/j.vascn.2021.107132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/12/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022]
Abstract
Opioid receptors are divided into the three classical types: MOP(μ:mu), DOP(δ:delta) and KOP(κ:kappa) that are naloxone-sensitive and an additional naloxone-insensitive nociceptin/orphanin FQ(N/OFQ) peptide receptor(NOP). Studies to determine opioid receptor location and turnover variably rely on; (i) measuring receptor mRNA, (ii) genetically tagging receptors, (iii) labelling receptors with radioligands, (iv) use of antibodies in immunohistochemistry/Western Blotting or (v) measuring receptor function coupled with the use of selective antagonists. All have their drawbacks with significant issues relating to mRNA not necessarily predicting protein, poor antibody selectivity and utility of radiolabels in low expression systems. In this minireview we discuss use of fluorescently labelled opioid receptor ligands. To maintain the pharmacological properties of the corresponding parent ligand fluorescently labelled ligands must take into account fluorophore (brightness and propensity to bleach), linker length and chemistry, and site to which the linker (and hence probe) will be attached. Use of donor and acceptor fluorophores with spectral overlap facilitates use in FRET type assays to determine proximity of ligand or tagged receptor pairs. There is a wide range of probes of agonist and antagonist nature for all four opioid receptor types; caution is needed with agonist probes due to the possibility for internalization. We have produced two novel ATTO based probes; DermorphinATTO488 (MOP) and N/OFQATTO594 (NOP). These probes label MOP and NOP in a range of preparations and using N/OFQATTO594 we demonstrate internalization and ligand-receptor interaction by FRET. Fluorescent opioid probes offer potential methodological advantages over more traditional use of antibodies and radiolabels.
Collapse
Affiliation(s)
- Despina Giakomidi
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Hodgkin Building, Leicester LE1 9HN. UK
| | - Mark F Bird
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Hodgkin Building, Leicester LE1 9HN. UK
| | - Remo Guerrini
- Department of Chemical, Pharmaceutical and Agricultural Sciences and LTTA, University of Ferrara, Italy
| | - Girolamo Calo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - David G Lambert
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Hodgkin Building, Leicester LE1 9HN. UK.
| |
Collapse
|
7
|
Waddington MA, Zheng X, Stauber JM, Hakim Moully E, Montgomery HR, Saleh LMA, Král P, Spokoyny AM. An Organometallic Strategy for Cysteine Borylation. J Am Chem Soc 2021; 143:8661-8668. [PMID: 34060827 DOI: 10.1021/jacs.1c02206] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Synthetic bioconjugation at cysteine (Cys) residues in peptides and proteins has emerged as a powerful tool in chemistry. Soft nucleophilicity of the sulfur in Cys renders an exquisite chemoselectivity with which various functional groups can be placed onto this residue under benign conditions. While a variety of reactions have been successful at producing Cys-based bioconjugates, the majority of these feature sulfur-carbon bonds. We report Cys-borylation, wherein a benchtop stable Pt(II)-based organometallic reagent can be used to transfer a boron-rich cluster onto a sulfur moiety in unprotected peptides forging a boron-sulfur bond. Cys-borylation proceeds at room temperature and tolerates a variety of functional groups present in complex polypeptides. Further, the bioconjugation strategy can be applied to a model protein modification of Cys-containing DARPin (designed ankyrin repeat protein). The resultant bioconjugates show no additional toxicity compared to their Cys alkyl-based congeners. Finally, we demonstrate how the developed Cys-borylation can enhance the proteolytic stability of the resultant peptide bioconjugates while maintaining the binding affinity to a protein target.
Collapse
Affiliation(s)
- Mary A Waddington
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Xin Zheng
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Julia M Stauber
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Elamar Hakim Moully
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Hayden R Montgomery
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Liban M A Saleh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Alexander M Spokoyny
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States.,California NanoSystems Institute (CNSI), University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095, United States
| |
Collapse
|
8
|
Mishra V. Affinity Tags for Protein Purification. Curr Protein Pept Sci 2021; 21:821-830. [PMID: 32504500 DOI: 10.2174/1389203721666200606220109] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 05/06/2020] [Indexed: 11/22/2022]
Abstract
The affinity tags are unique proteins/peptides that are attached at the N- or C-terminus of the recombinant proteins. These tags help in protein purification. Additionally, some affinity tags also serve a dual purpose as solubility enhancers for challenging protein targets. By applying a combinatorial approach, carefully chosen affinity tags designed in tandem have proven to be very successful in the purification of single proteins or multi-protein complexes. In this mini-review, the key features of the most commonly used affinity tags are discussed. The affinity tags have been classified into two significant categories, epitope tags, and protein/domain tags. The epitope tags are generally small peptides with high affinity towards a chromatography resin. The protein/domain tags often perform double duty as solubility enhancers as well as aid in affinity purification. Finally, protease-based affinity tag removal strategies after purification are discussed.
Collapse
Affiliation(s)
- Vibhor Mishra
- Department of Biology, Indiana University, Bloomington, IN 47405, USA,Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
9
|
Giakomidi D, Bird MF, McDonald J, Marzola E, Guerrini R, Chanoch S, Sabu N, Horley B, Calo G, Lambert DG. Evaluation of [Cys(ATTO 488)8]Dermorphin-NH2 as a novel tool for the study of μ-opioid peptide receptors. PLoS One 2021; 16:e0250011. [PMID: 33891604 PMCID: PMC8064508 DOI: 10.1371/journal.pone.0250011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 11/26/2022] Open
Abstract
The μ-opioid peptide (MOP) receptor is a member of the opioid receptor family and an important clinical target for analgesia. Measuring MOP receptor location and tracking its turnover traditionally used radiolabels or antibodies with attendant problems of utility of radiolabels in whole cells and poor antibody selectivity. To address these issues we have synthesized and characterised a novel ATTO488 based fluorescent Dermorphin analogue; [Cys(ATTO 488)8]Dermorphin-NH2 (DermATTO488). We initially assessed the binding profile of DermATTO488 in HEK cells expressing human MOP and CHO cells expressing human MOP, δ-opioid peptide (DOP), κ-opioid peptide (KOP) and Nociceptin/Orphanin FQ peptide (NOP) receptors using radioligand binding. Functional activity of the conjugated peptide was assessed by measuring (i) the ability of the ligand to engage G-protein by measuring the ability to stimulate GTPγ[35S] binding and (ii) the ability to stimulate phosphorylation of ERK1/2. Receptor location was visualised using confocal scanning laser microscopy. Dermorphin and DermATTO488 bound to HEKMOP (pKi: 8.29 and 7.00; p<0.05), CHOMOP (pKi: 9.26 and 8.12; p<0.05) and CHODOP (pKi: 7.03 and 7.16; p>0.05). Both ligands were inactive at KOP and NOP. Dermorphin and DermATTO488 stimulated the binding of GTPγ[35S] with similar pEC50 (7.84 and 7.62; p>0.05) and Emax (1.52 and 1.34fold p>0.05) values. Moreover, Dermorphin and DermATTO488 produced a monophasic stimulation of ERK1/2 phosphorylation peaking at 5mins (6.98 and 7.64-fold; p>0.05). Finally, in confocal microscopy DermATTO488 bound to recombinant MOP receptors on CHO and HEK cells in a concentration dependent manner that could be blocked by pre-incubation with unlabelled Dermorphin or Naloxone. Collectively, addition to ATTO488 to Dermorphin produced a ligand not dissimilar to Dermorphin; with ~10fold selectivity over DOP. This new ligand DermATTO488 retained functional activity and could be used to visualise MOP receptor location.
Collapse
Affiliation(s)
- Despina Giakomidi
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Mark F. Bird
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - John McDonald
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Erika Marzola
- Department of Chemical and Pharmaceutical Sciences and LTTA, University of Ferrara, Ferrara, Italy
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences and LTTA, University of Ferrara, Ferrara, Italy
| | - Serena Chanoch
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Nidhuna Sabu
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Barbara Horley
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
| | - Girolamo Calo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - David G. Lambert
- Department of Cardiovascular Sciences (Anaesthesia, Critical Care and Pain Management), University of Leicester, Leicester Royal Infirmary, Leicester, United Kingdom
- * E-mail:
| |
Collapse
|
10
|
Schmidt TGM, Eichinger A, Schneider M, Bonet L, Carl U, Karthaus D, Theobald I, Skerra A. The Role of Changing Loop Conformations in Streptavidin Versions Engineered for High-affinity Binding of the Strep-tag II Peptide. J Mol Biol 2021; 433:166893. [PMID: 33639211 DOI: 10.1016/j.jmb.2021.166893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/25/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
The affinity system based on the artificial peptide ligand Strep-tag® II and engineered tetrameric streptavidin, known as Strep-Tactin®, offers attractive applications for the study of recombinant proteins, from detection and purification to functional immobilization. To further improve binding of the Strep-tag II to streptavidin we have subjected two protruding loops that shape its ligand pocket for the peptide - instead of D-biotin recognized by the natural protein - to iterative random mutagenesis. Sequence analyses of hits from functional screening assays revealed several unexpected structural motifs, such as a disulfide bridge at the base of one loop, replacement of the crucial residue Trp120 by Gly and a two-residue deletion in the second loop. The mutant m1-9 (dubbed Strep-Tactin XT) showed strongly enhanced affinity towards the Strep-tag II, which was further boosted in case of the bivalent Twin-Strep-tag®. Four representative streptavidin mutants were crystallized in complex with the Strep-tag II peptide and their X-ray structures were solved at high resolutions. In addition, the crystal structure of the complex between Strep-Tactin XT and the Twin-Strep-tag was elucidated, indicating a bivalent mode of binding and explaining the experimentally observed avidity effect. Our study illustrates the structural plasticity of streptavidin as a scaffold for ligand binding and reveals interaction modes that would have been difficult to predict. As result, Strep-Tactin XT offers a convenient reagent for the kinetically stable immobilization of recombinant proteins fused with the Twin-Strep-tag. The possibility of reversibly dissociating such complexes simply with D-biotin as a competing ligand enables functional studies in protein science as well as cell biology.
Collapse
Affiliation(s)
| | - Andreas Eichinger
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany
| | - Markus Schneider
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany
| | - Lidia Bonet
- IBA GmbH, Rudolf-Wissell-Str. 28, 37079 Göttingen, Germany
| | - Uwe Carl
- IBA GmbH, Rudolf-Wissell-Str. 28, 37079 Göttingen, Germany
| | | | - Ina Theobald
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany.
| |
Collapse
|
11
|
Ranawakage DC, Okada K, Sugio K, Kawaguchi Y, Kuninobu-Bonkohara Y, Takada T, Kamachi Y. Efficient CRISPR-Cas9-Mediated Knock-In of Composite Tags in Zebrafish Using Long ssDNA as a Donor. Front Cell Dev Biol 2021; 8:598634. [PMID: 33681181 PMCID: PMC7928300 DOI: 10.3389/fcell.2020.598634] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the unprecedented gene editing capability of CRISPR-Cas9-mediated targeted knock-in, the efficiency and precision of this technology still require further optimization, particularly for multicellular model organisms, such as the zebrafish (Danio rerio). Our study demonstrated that an ∼200 base-pair sequence encoding a composite tag can be efficiently "knocked-in" into the zebrafish genome using a combination of the CRISPR-Cas9 ribonucleoprotein complex and a long single-stranded DNA (lssDNA) as a donor template. Here, we targeted the sox3, sox11a, and pax6a genes to evaluate the knock-in efficiency of lssDNA donors with different structures in somatic cells of injected embryos and for their germline transmission. The structures and sequence characteristics of the lssDNA donor templates were found to be crucial to achieve a high rate of precise and heritable knock-ins. The following were our key findings: (1) lssDNA donor strand selection is important; however, strand preference and its dependency appear to vary among the target loci or their sequences. (2) The length of the 3' homology arm of the lssDNA donor affects knock-in efficiency in a site-specific manner; particularly, a shorter 50-nt arm length leads to a higher knock-in efficiency than a longer 300-nt arm for the sox3 and pax6a knock-ins. (3) Some DNA sequence characteristics of the knock-in donors and the distance between the CRISPR-Cas9 cleavage site and the tag insertion site appear to adversely affect the repair process, resulting in imprecise editing. By implementing the proposed method, we successfully obtained precisely edited sox3, sox11a, and pax6a knock-in alleles that contained a composite tag composed of FLAGx3 (or PAx3), Bio tag, and HiBiT tag (or His tag) with moderate to high germline transmission rates as high as 21%. Furthermore, the knock-in allele-specific quantitative polymerase chain reaction (qPCR) for both the 5' and 3' junctions indicated that knock-in allele frequencies were higher at the 3' side of the lssDNAs, suggesting that the lssDNA-templated knock-in was mediated by unidirectional single-strand template repair (SSTR) in zebrafish embryos.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Yusuke Kamachi
- School of Environmental Science and Engineering, Kochi University of Technology, Kochi, Japan
| |
Collapse
|
12
|
Nilvebrant J, Åstrand M, Hober S. An Orthogonal Fusion Tag for Efficient Protein Purification. Methods Mol Biol 2021; 2178:159-166. [PMID: 33128750 DOI: 10.1007/978-1-0716-0775-6_13] [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: 06/11/2023]
Abstract
In this chapter, we present an efficient method for stringent protein purification facilitated by a dual affinity tag referred to as ABDz1, which is based on a 5 kDa albumin-binding domain from Streptococcal Protein G. The small fusion tag enables an orthogonal affinity purification approach based on two successive and highly specific affinity purification steps. This approach is enabled by native binding of ABDz1 to human serum albumin and engineered binding to Staphylococcal Protein A, respectively. The ABDz1-tag can be fused to either terminus of a protein of interest and the purification steps can be carried out using standard laboratory equipment.
Collapse
Affiliation(s)
- Johan Nilvebrant
- Division of Protein Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH/AlbaNova University Center, Stockholm, Sweden
| | - Mikael Åstrand
- Division of Protein Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH/AlbaNova University Center, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry Biotechnology and Health (CBH), AlbaNova University Center, Stockholm, Sweden.
| |
Collapse
|
13
|
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: 30] [Impact Index Per Article: 7.5] [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.
Collapse
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
| |
Collapse
|
14
|
Appaiah P, Vasu P. Improvement, cloning, and expression of an in silico designed protein enriched with large neutral amino acids in Pichia pastoris for possible application in phenylketonuria. J Food Biochem 2020; 44:e13151. [PMID: 31960483 DOI: 10.1111/jfbc.13151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/25/2019] [Accepted: 12/28/2019] [Indexed: 11/29/2022]
Abstract
Phenylketonuria (PKU) is an inborn disease caused by defective phenylalanine hydroxylase, which consequently results in the accumulation of phenylalanine in the brain leading to further complications. One of the promising approaches in dietary treatment is the supplementation of large neutral amino acid (LNAA). The LNAA compete with phenylalanine for the common L-type LNAA transporter across the blood-brain barrier, and decrease phenylalanine levels in the brain. In this study, the earlier LNAA-enriched protein model was improved (Protein Model-66) and validated in silico. The reverse translated and codon-optimized synthetic LNAA66 gene was cloned into pPICZαC and expressed in Pichia pastoris. The expressed protein was purified by His Select affinity chromatography. SDS-PAGE and Western blotting analysis showed a band at an expected molecular weight of 12 kDa, confirming the expression of the modeled protein. To our knowledge, this is the first report showing the cloning and expression of an in silico designed LNAA-enriched protein. PRACTICAL APPLICATIONS: One of the promising dietary treatment of phenylketonuria (PKU) is the supplementation of large neutral amino acid (LNAA), wherein high levels of LNAA compete with phenylalanine for the same L-type LNAA transporter, and consequently decrease phenylalanine accumulation in the brain, thereby decreasing neurological complications. For the first time, here, we are showing that an in silico designed and validated Protein Model-66, rich in LNAA, can be successfully cloned and expressed in Pichia pastoris. The complete biochemical and structural characterization of this protein will give a clear insight into its potential application for PKU treatment. The protein can be potentially used as a supplement to treat PKU to those who are non-adherent to the restricted, non-palatable, and expensive diet. Furthermore, this novel and effective strategy of in silico designing, cloning and expression can be exploited to develop proteins for various applications of industrial, food, medical, and academic relevance.
Collapse
Affiliation(s)
- Prakruthi Appaiah
- Department of Food Safety and Analytical Quality Control Laboratory, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prasanna Vasu
- Department of Food Safety and Analytical Quality Control Laboratory, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
15
|
Becker W, Wimberger F, Zangger K. Vibrio natriegens: An Alternative Expression System for the High-Yield Production of Isotopically Labeled Proteins. Biochemistry 2019; 58:2799-2803. [DOI: 10.1021/acs.biochem.9b00403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Walter Becker
- Institute of Chemistry, University of Graz, Graz 8010, Austria
| | | | - Klaus Zangger
- Institute of Chemistry, University of Graz, Graz 8010, Austria
| |
Collapse
|
16
|
DeCaprio J, Kohl TO. Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies. Cold Spring Harb Protoc 2019; 2019:2019/2/pdb.prot098657. [PMID: 30710027 DOI: 10.1101/pdb.prot098657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10-15) to attomole (10-18) range is required to be of exceptional purity. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP). In TAP, the cDNA of the target protein is engineered to contain at least two different epitope tags, and the target protein is extracted under nondenaturing conditions upon expression using an appropriate protein expression platform (CHO cells, HEK 293 cells, or yeast). The expressed protein is initially immunoprecipitated using an antibody against one epitope tag and is eluted in the presence of excess peptide by competition for antibody-binding sites, before being reimmunoprecipitated using an antibody that specifically recognizes the second epitope. These sequential immunoprecipitations significantly reduce the presence of associated nonspecific proteins. Numerous combinations of epitope tags have been applied for tandem affinity purification, and this protocol illustrates the use of tandem hemagglutinin (HA) and FLAG epitope tags. The first immunoprecipitation uses an anti-FLAG antibody followed by the elution in the presence of a competing FLAG peptide before the reimmunoprecipitation of the protein using an anti-HA antibody. Numerous high-quality antiepitope tag antibodies are commercially available from different antibody manufacturers.
Collapse
|
17
|
Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
Collapse
Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| |
Collapse
|
18
|
Bernier SC, Cantin L, Salesse C. Systematic analysis of the expression, solubility and purification of a passenger protein in fusion with different tags. Protein Expr Purif 2018; 152:92-106. [DOI: 10.1016/j.pep.2018.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/19/2018] [Indexed: 12/31/2022]
|
19
|
Sciuto MR, Coppola V, Iannolo G, De Maria R, Haas TL. Two-Step Co-Immunoprecipitation (TIP). ACTA ACUST UNITED AC 2018; 125:e80. [DOI: 10.1002/cpmb.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Maria Rita Sciuto
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità; Rome Italy
| | - Valeria Coppola
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità; Rome Italy
| | - Gioacchin Iannolo
- Regenerative Medicine and Biomedical Technologies Unit, Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT; Palermo Italy
| | - Ruggero De Maria
- Institute of General Pathology, Università Cattolica del Sacro Cuore; Rome Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS; Rome Italy
| | - Tobias L. Haas
- Institute of General Pathology, Università Cattolica del Sacro Cuore; Rome Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS; Rome Italy
| |
Collapse
|
20
|
Kriznik A, Yéléhé‐Okouma M, Lec J, Groshenry G, Le Cordier H, Charron C, Quinternet M, Mazon H, Talfournier F, Boschi‐Muller S, Jouzeau J, Reboul P. CRDSATGenerated by pCARGHO: A New Efficient Lectin‐Based Affinity Tag Method for Safe, Simple, and Low‐Cost Protein Purification. Biotechnol J 2018; 14:e1800214. [DOI: 10.1002/biot.201800214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/28/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Alexandre Kriznik
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| | - Mélissa Yéléhé‐Okouma
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
- Département de Pharmacologie Clinique et ToxicologieCentre Hospitalier Régional UniversitaireF‐54000NancyFrance
| | - Jean‐Christophe Lec
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| | - Guillaume Groshenry
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| | - Hélène Le Cordier
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| | - Christophe Charron
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| | - Marc Quinternet
- Unité Mixte de Service (UMS) 2008Ingénierie Biologie Santé en Lorraine (IBSLor)F‐54000NancyFrance
| | - Hortense Mazon
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| | - François Talfournier
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| | - Sandrine Boschi‐Muller
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| | - Jean‐Yves Jouzeau
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
- Département de Pharmacologie Clinique et ToxicologieCentre Hospitalier Régional UniversitaireF‐54000NancyFrance
| | - Pascal Reboul
- Université de LorraineCNRS, Ingénierie Moléculaire et Pathologie Articulaire (IMoPA)F‐54000NancyFrance
| |
Collapse
|
21
|
Mhurchú NN, Zoubak L, McGauran G, Linse S, Yeliseev A, O’Connell DJ. Simplifying G Protein-Coupled Receptor Isolation with a Calcium-Dependent Fragment Complementation Affinity System. Biochemistry 2018; 57:4383-4390. [DOI: 10.1021/acs.biochem.8b00469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Niamh Ní Mhurchú
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin D04 V1W8, Ireland
| | - Lioudmila Zoubak
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Bethesda, Maryland 20892, United States
| | - Gavin McGauran
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin D04 V1W8, Ireland
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Box 118, Lund 221 00, Sweden
| | - Alexei Yeliseev
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Bethesda, Maryland 20892, United States
| | - David J. O’Connell
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin D04 V1W8, Ireland
| |
Collapse
|
22
|
Mugabo Y, Sadeghi M, Fang NN, Mayor T, Lim GE. Elucidation of the 14-3-3ζ interactome reveals critical roles of RNA-splicing factors during adipogenesis. J Biol Chem 2018. [PMID: 29530978 DOI: 10.1074/jbc.m117.816272] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adipogenesis involves a complex signaling network requiring strict temporal and spatial organization of effector molecules. Molecular scaffolds, such as 14-3-3 proteins, facilitate such organization, and we have previously identified 14-3-3ζ as an essential scaffold in adipocyte differentiation. The interactome of 14-3-3ζ is large and diverse, and it is possible that novel adipogenic factors may be present within it, but this possibility has not yet been tested. Herein, we generated mouse embryonic fibroblasts from mice overexpressing a tandem affinity purification (TAP) epitope-tagged 14-3-3ζ molecule. After inducing adipogenesis, TAP-14-3-3ζ complexes were purified, followed by MS analysis to determine the 14-3-3ζ interactome. We observed more than 100 proteins that were unique to adipocyte differentiation, 56 of which were novel interacting partners. Among these, we were able to identify previously established regulators of adipogenesis (i.e. Ptrf/Cavin1) within the 14-3-3ζ interactome, confirming the utility of this approach to detect adipogenic factors. We found that proteins related to RNA metabolism, processing, and splicing were enriched in the interactome. Analysis of transcriptomic data revealed that 14-3-3ζ depletion in 3T3-L1 cells affected alternative splicing of mRNA during adipocyte differentiation. siRNA-mediated depletion of RNA-splicing factors within the 14-3-3ζ interactome, that is, of Hnrpf, Hnrpk, Ddx6, and Sfpq, revealed that they have essential roles in adipogenesis and in the alternative splicing of Pparg and the adipogenesis-associated gene Lpin1 In summary, we have identified novel adipogenic factors within the 14-3-3ζ interactome. Further characterization of additional proteins within the 14-3-3ζ interactome may help identify novel targets to block obesity-associated expansion of adipose tissues.
Collapse
Affiliation(s)
- Yves Mugabo
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada.,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
| | - Mina Sadeghi
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada.,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
| | - Nancy N Fang
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Thibault Mayor
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Gareth E Lim
- From the Centre Hospitalier de l'Université de Montréal, Montréal, Québec H2X 029, Canada, .,the Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada, and
| |
Collapse
|
23
|
Abstract
Immunoprecipitation is one of the most important and widely used techniques for the detection and purification of a protein of interest. Thanks to highly specific interaction between antigen and antibody, a target protein is purified and concentrated effectively. To obtain reasonable amounts of a target protein, it is crucially important to prepare total cell lysates in which the target protein is present in a soluble form. Here, we describe methods to prepare total cell lysates of fission yeast, which are then used directly for immunoprecipitation. We also describe some tips to select reagents for preparing buffers having a substantial impact on protein solubility, because there is essentially no reagent that can accommodate the full range of proteins having different characteristics.
Collapse
|
24
|
Bassard JE, Halkier BA. How to prove the existence of metabolons? PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2018; 17:211-227. [PMID: 29755303 PMCID: PMC5932110 DOI: 10.1007/s11101-017-9509-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/19/2017] [Indexed: 05/21/2023]
Abstract
Sequential enzymes in biosynthetic pathways are organized in metabolons. It is challenging to provide experimental evidence for the existence of metabolons as biosynthetic pathways are composed of highly dynamic protein-protein interactions. Many different methods are being applied, each with strengths and weaknesses. We will present and evaluate several techniques that have been applied in providing evidence for the orchestration of the biosynthetic pathways of cyanogenic glucosides and glucosinolates in metabolons. These evolutionarily related pathways have ER-localized cytochromes P450 that are proposed to function as anchoring site for assembly of the enzymes into metabolons. Additionally, we have included commonly used techniques, even though they have not been used (yet) on these two pathways. In the review, special attention will be given to less-exploited fluorescence-based methods such as FCS and FLIM. Ultimately, understanding the orchestration of biosynthetic pathways may contribute to successful engineering in heterologous hosts.
Collapse
Affiliation(s)
- Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
25
|
Sciuto MR, Warnken U, Schnölzer M, Valvo C, Brunetto L, Boe A, Biffoni M, Krammer PH, De Maria R, Haas TL. Two-Step Coimmunoprecipitation (TIP) Enables Efficient and Highly Selective Isolation of Native Protein Complexes. Mol Cell Proteomics 2017; 17:993-1009. [PMID: 29217617 DOI: 10.1074/mcp.o116.065920] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 11/22/2017] [Indexed: 11/06/2022] Open
Abstract
Coimmunoprecipitation (co-IP) is one of the most frequently used techniques to study protein-protein (PPIs) or protein-nucleic acid interactions (PNIs). However, the presence of coprecipitated contaminants is a well-recognized issue associated with single-step co-IPs. To overcome this limitation, we developed the two-step co-IP (TIP) strategy that enables sequential coimmunoprecipitations of endogenous protein complexes. TIP can be performed with a broad range of mono- and polyclonal antibodies targeting a single protein or different components of a given complex. TIP results in a highly selective enrichment of protein complexes and thus outperforms single-step co-IPs for downstream applications such as mass spectrometry for the identification of PPIs and quantitative PCR for the analysis of PNIs. We benchmarked TIP for the identification of CD95/FAS-interacting proteins in primary human CD4+ T cells, which recapitulated all major known interactors, but also enabled the proteomics discovery of PPM1G and IPO7 as new interaction partners. For its feasibility and high performance, we propose TIP as an advanced tool for the isolation of highly purified protein-protein and protein-nucleic acid complexes under native expression conditions.
Collapse
Affiliation(s)
- Maria Rita Sciuto
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy;
| | - Uwe Warnken
- §Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Martina Schnölzer
- §Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Cecilia Valvo
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.,¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| | - Lidia Brunetto
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandra Boe
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Mauro Biffoni
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Peter H Krammer
- ‖Department of Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ruggero De Maria
- ¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| | - Tobias L Haas
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy; .,¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| |
Collapse
|
26
|
Jia B, Jeon CO. High-throughput recombinant protein expression in Escherichia coli: current status and future perspectives. Open Biol 2017; 6:rsob.160196. [PMID: 27581654 PMCID: PMC5008019 DOI: 10.1098/rsob.160196] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/03/2016] [Indexed: 12/26/2022] Open
Abstract
The ease of genetic manipulation, low cost, rapid growth and number of previous studies have made Escherichia coli one of the most widely used microorganism species for producing recombinant proteins. In this post-genomic era, challenges remain to rapidly express and purify large numbers of proteins for academic and commercial purposes in a high-throughput manner. In this review, we describe several state-of-the-art approaches that are suitable for the cloning, expression and purification, conducted in parallel, of numerous molecules, and we discuss recent progress related to soluble protein expression, mRNA folding, fusion tags, post-translational modification and production of membrane proteins. Moreover, we address the ongoing efforts to overcome various challenges faced in protein expression in E. coli, which could lead to an improvement of the current system from trial and error to a predictable and rational design.
Collapse
Affiliation(s)
- Baolei Jia
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| |
Collapse
|
27
|
Xu Z, Rui YN, Balzeau J, Menezes MR, Niu A, Hagan JP, Kim DH. Highly efficient one-step scarless protein tagging by type IIS restriction endonuclease-mediated precision cloning. Biochem Biophys Res Commun 2017; 490:8-16. [PMID: 28576485 DOI: 10.1016/j.bbrc.2017.05.153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 05/26/2017] [Indexed: 12/22/2022]
Abstract
Protein tagging with a wide variety of epitopes and/or fusion partners is used routinely to dissect protein function molecularly. Frequently, the required DNA subcloning is inefficient, especially in cases where multiple constructs are desired for a given protein with unique tags. Additionally, the generated clones have unwanted junction sequences introduced. To add versatile tags into the extracellular domain of the transmembrane protein THSD1, we developed a protein tagging technique that utilizes non-classical type IIS restriction enzymes that recognize non-palindromic DNA sequences and cleave outside of their recognition sites. Our results demonstrate that this method is highly efficient and can precisely fuse any tag into any position of a protein in a scarless manner. Moreover, this method is cost-efficient and adaptable because it uses commercially available type IIS restriction enzymes and is compatible with the traditional cloning system used by many labs. Therefore, precision tagging technology will benefit a number of researchers by providing an alternate method to integrate an array of tags into protein expression constructs.
Collapse
Affiliation(s)
- Zhen Xu
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States.
| | - Yan-Ning Rui
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - Julien Balzeau
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - Miriam R Menezes
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - Airu Niu
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - John P Hagan
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States
| | - Dong H Kim
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, TX, United States.
| |
Collapse
|
28
|
Abstract
Affibody molecules can be used as tools for molecular recognition in diagnostic and therapeutic applications. There are several preclinical studies reported on diagnostic and therapeutic use of this molecular class of alternative scaffolds, and early clinical evidence is now beginning to accumulate that suggests the Affibody molecules to be efficacious and safe in man. The small size and ease of engineering make Affibody molecules suitable for use in multispecific constructs where AffiMabs is one such that offers the option to potentiate antibodies for use in complex disease.
Collapse
|
29
|
Liu R, Liu T, Wei W, Guo K, Yang N, Tian S, Zhu J, Liu Y, Zhou W, Yang H. Novel interacting proteins identified by tandem affinity purification coupled to nano LC–MS/MS interact with ribosomal S6 protein kinase 4 (RSK4) and its variant protein (RSK4m). Int J Biol Macromol 2017; 96:421-428. [DOI: 10.1016/j.ijbiomac.2016.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 12/16/2022]
|
30
|
Yadav DK, Yadav N, Yadav S, Haque S, Tuteja N. An insight into fusion technology aiding efficient recombinant protein production for functional proteomics. Arch Biochem Biophys 2016; 612:57-77. [DOI: 10.1016/j.abb.2016.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
|
31
|
Goossens J, De Geyter N, Walton A, Eeckhout D, Mertens J, Pollier J, Fiallos-Jurado J, De Keyser A, De Clercq R, Van Leene J, Gevaert K, De Jaeger G, Goormachtig S, Goossens A. Isolation of protein complexes from the model legume Medicago truncatula by tandem affinity purification in hairy root cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:476-489. [PMID: 27377668 DOI: 10.1111/tpj.13258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/21/2016] [Accepted: 06/30/2016] [Indexed: 05/26/2023]
Abstract
Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most powerful techniques to isolate protein complexes and elucidate protein interaction networks. Here, we describe the development of a TAP-MS strategy for the model legume Medicago truncatula, which is widely studied for its ability to produce valuable natural products and to engage in endosymbiotic interactions. As biological material, transgenic hairy roots, generated through Agrobacterium rhizogenes-mediated transformation of M. truncatula seedlings, were used. As proof of concept, proteins involved in the cell cycle, transcript processing and jasmonate signalling were chosen as bait proteins, resulting in a list of putative interactors, many of which confirm the interologue concept of protein interactions, and which can contribute to biological information about the functioning of these bait proteins in planta. Subsequently, binary protein-protein interactions among baits and preys, and among preys were confirmed by a systematic yeast two-hybrid screen. Together, by establishing a M. truncatula TAP-MS platform, we extended the molecular toolbox of this model species.
Collapse
Affiliation(s)
- Jonas Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Nathan De Geyter
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jan Mertens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jennifer Fiallos-Jurado
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Annick De Keyser
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| |
Collapse
|
32
|
O’Brien J, Shea KJ. Tuning the Protein Corona of Hydrogel Nanoparticles: The Synthesis of Abiotic Protein and Peptide Affinity Reagents. Acc Chem Res 2016; 49:1200-10. [PMID: 27254382 DOI: 10.1021/acs.accounts.6b00125] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Nanomaterials, when introduced into a complex, protein-rich environment, rapidly acquire a protein corona. The type and amount of proteins that constitute the corona depend significantly on the synthetic identity of the nanomaterial. For example, hydrogel nanoparticles (NPs) such as poly(N-isopropylacrylamide) (NIPAm) have little affinity for plasma proteins; in contrast, carboxylated poly(styrene) NPs acquire a dense protein corona. This range of protein adsorption suggests that the protein corona might be "tuned" by controlling the chemical composition of the NP. In this Account, we demonstrate that small libraries of synthetic polymer NPs incorporating a diverse pool of functional monomers can be screened for candidates with high affinity and selectivity to targeted biomacromolecules. Through directed synthetic evolution of NP compositions, one can tailor the protein corona to create synthetic organic hydrogel polymer NPs with high affinity and specificity to peptide toxins, enzymes, and other functional proteins, as well as to specific domains of large proteins. In addition, many NIPAm NPs undergo a change in morphology as a function of temperature. This transformation often correlates with a significant change in NP-biomacromolecule affinity, resulting in a temperature-dependent protein corona. This temperature dependence has been used to develop NP hydrogels with autonomous affinity switching for the protection of proteins from thermal stress and as a method of biomacromolecule purification through a selective thermally induced catch and release. In addition to temperature, changes in pH or buffer can also alter a NP protein corona composition, a property that has been exploited for protein purification. Finally, synthetic polymer nanoparticles with low nanomolar affinity for a peptide toxin were shown to capture and neutralize the toxin in the bloodstream of living mice. While the development of synthetic polymer alternatives to protein affinity reagents is in its early stages, these recent successes using only small libraries of functional monomers are most encouraging. It is likely that by expanding the chemical diversity of functional hydrogels and other polymers, a much broader range of NP-biomacromolecule affinity pairs will result. Since these robust, nontoxic polymers are readily synthesized in the chemistry laboratory, we believe the results presented in this Account offer a promising future for the development of low cost alternatives to more traditional protein affinity reagents such as antibodies.
Collapse
Affiliation(s)
- Jeffrey O’Brien
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Kenneth J. Shea
- Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| |
Collapse
|
33
|
Buntru A, Trepte P, Klockmeier K, Schnoegl S, Wanker EE. Current Approaches Toward Quantitative Mapping of the Interactome. Front Genet 2016; 7:74. [PMID: 27200083 PMCID: PMC4854875 DOI: 10.3389/fgene.2016.00074] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
Protein–protein interactions (PPIs) play a key role in many, if not all, cellular processes. Disease is often caused by perturbation of PPIs, as recently indicated by studies of missense mutations. To understand the associations of proteins and to unravel the global picture of PPIs in the cell, different experimental detection techniques for PPIs have been established. Genetic and biochemical methods such as the yeast two-hybrid system or affinity purification-based approaches are well suited to high-throughput, proteome-wide screening and are mainly used to obtain qualitative results. However, they have been criticized for not reflecting the cellular situation or the dynamic nature of PPIs. In this review, we provide an overview of various genetic methods that go beyond qualitative detection and allow quantitative measuring of PPIs in mammalian cells, such as dual luminescence-based co-immunoprecipitation, Förster resonance energy transfer or luminescence-based mammalian interactome mapping with bait control. We discuss the strengths and weaknesses of different techniques and their potential applications in biomedical research.
Collapse
Affiliation(s)
| | - Philipp Trepte
- Max Delbrueck Center for Molecular Medicine Berlin, Germany
| | | | | | - Erich E Wanker
- Max Delbrueck Center for Molecular Medicine Berlin, Germany
| |
Collapse
|
34
|
Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016; 11:738-56. [PMID: 26864455 PMCID: PMC7162211 DOI: 10.1002/cmdc.201500495] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/08/2016] [Indexed: 12/14/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
Collapse
Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
| |
Collapse
|
35
|
Zhou M, Li Q, Wang R. Current Experimental Methods for Characterizing Protein-Protein Interactions. ChemMedChem 2016. [PMID: 26864455 DOI: 10.1002/cmdc.201500495.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein molecules often interact with other partner protein molecules in order to execute their vital functions in living organisms. Characterization of protein-protein interactions thus plays a central role in understanding the molecular mechanism of relevant protein molecules, elucidating the cellular processes and pathways relevant to health or disease for drug discovery, and charting large-scale interaction networks in systems biology research. A whole spectrum of methods, based on biophysical, biochemical, or genetic principles, have been developed to detect the time, space, and functional relevance of protein-protein interactions at various degrees of affinity and specificity. This article presents an overview of these experimental methods, outlining the principles, strengths and limitations, and recent developments of each type of method.
Collapse
Affiliation(s)
- Mi Zhou
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Qing Li
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Rd, Shanghai, 200032, People's Republic of China. .,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Macau, 999078, People's Republic of China.
| |
Collapse
|
36
|
Sari D, Gupta K, Thimiri Govinda Raj DB, Aubert A, Drncová P, Garzoni F, Fitzgerald D, Berger I. The MultiBac Baculovirus/Insect Cell Expression Vector System for Producing Complex Protein Biologics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 896:199-215. [PMID: 27165327 PMCID: PMC7122245 DOI: 10.1007/978-3-319-27216-0_13] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multiprotein complexes regulate most if not all cellular functions. Elucidating the structure and function of these complex cellular machines is essential for understanding biology. Moreover, multiprotein complexes by themselves constitute powerful reagents as biologics for the prevention and treatment of human diseases. Recombinant production by the baculovirus/insect cell expression system is particularly useful for expressing proteins of eukaryotic origin and their complexes. MultiBac, an advanced baculovirus/insect cell system, has been widely adopted in the last decade to produce multiprotein complexes with many subunits that were hitherto inaccessible, for academic and industrial research and development. The MultiBac system, its development and numerous applications are presented. Future opportunities for utilizing MultiBac to catalyze discovery are outlined.
Collapse
Affiliation(s)
- Duygu Sari
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
- Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - Kapil Gupta
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
- Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - Deepak Balaji Thimiri Govinda Raj
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
- Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - Alice Aubert
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
- Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - Petra Drncová
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
- Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - Frederic Garzoni
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
- Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France
| | - Daniel Fitzgerald
- Geneva Biotech SARL, Avenue de la Roseraie 64, 1205, Genève, Switzerland
| | - Imre Berger
- European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France.
- Unit of Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, UMI 3265, 71 avenue des Martyrs, 38042, Grenoble Cedex 9, France.
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
| |
Collapse
|
37
|
Yin LL, Wang SP, Shan XN, Zhang ST, Tao NJ. Quantification of protein interaction kinetics in a micro droplet. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:114101. [PMID: 26628149 PMCID: PMC4636506 DOI: 10.1063/1.4934802] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
Characterization of protein interactions is essential to the discovery of disease biomarkers, the development of diagnostic assays, and the screening for therapeutic drugs. Conventional flow-through kinetic measurements need relative large amount of sample that is not feasible for precious protein samples. We report a novel method to measure protein interaction kinetics in a single droplet with sub microliter or less volume. A droplet in a humidity-controlled environmental chamber is replacing the microfluidic channels as the reactor for the protein interaction. The binding process is monitored by a surface plasmon resonance imaging (SPRi) system. Association curves are obtained from the average SPR image intensity in the center area of the droplet. The washing step required by conventional flow-through SPR method is eliminated in the droplet method. The association and dissociation rate constants and binding affinity of an antigen-antibody interaction are obtained by global fitting of association curves at different concentrations. The result obtained by this method is accurate as validated by conventional flow-through SPR system. This droplet-based method not only allows kinetic studies for proteins with limited supply but also opens the door for high-throughput protein interaction study in a droplet-based microarray format that enables measurement of many to many interactions on a single chip.
Collapse
Affiliation(s)
- L L Yin
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - S P Wang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - X N Shan
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - S T Zhang
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| | - N J Tao
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| |
Collapse
|
38
|
Abstract
![]()
Exploration of protein function and
interaction is critical for
discovering links among genomics, proteomics, and disease state; yet,
the immense complexity of proteomics found in biological systems currently
limits our investigational capacity. Although affinity and autofluorescent
tags are widely employed for protein analysis, these methods have
been met with limited success because they lack specificity and require
multiple fusion tags and genetic constructs. As an alternative approach,
the innovative HaloTag protein fusion platform allows protein function
and interaction to be comprehensively analyzed using a single genetic
construct with multiple capabilities. This is accomplished using a
simplified process, in which a variable HaloTag ligand binds rapidly
to the HaloTag protein (usually linked to the protein of interest)
with high affinity and specificity. In this review, we examine all
current applications of the HaloTag technology platform for biomedical
applications, such as the study of protein isolation and purification,
protein function, protein–protein and protein–DNA interactions,
biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the
HaloTag platform are briefly discussed along with potential future
applications.
Collapse
Affiliation(s)
- Christopher G England
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Haiming Luo
- ‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weibo Cai
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,§University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53705, United States
| |
Collapse
|
39
|
Cryo-Electron Microscopy Structure of Human Peroxiredoxin-3 Filament Reveals the Assembly of a Putative Chaperone. Structure 2015; 23:912-920. [DOI: 10.1016/j.str.2015.03.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/21/2015] [Accepted: 03/23/2015] [Indexed: 01/07/2023]
|
40
|
Bigeard J, Pflieger D, Colcombet J, Gérard L, Mireau H, Hirt H. Protein complexes characterization in Arabidopsis thaliana by tandem affinity purification coupled to mass spectrometry analysis. Methods Mol Biol 2015; 1171:237-50. [PMID: 24908132 DOI: 10.1007/978-1-4939-0922-3_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Proteins are major elements participating in all the key functions of the cells. They rarely fulfill their physiological roles in an autonomous way but rather act as part of more complex cellular machines. Indeed they can bind different types of molecules (proteins, nucleic acids, metabolites, etc.), via stable or transient interactions, depending on their nature and functions. The identification of the molecular partners of a given protein is hence essential to better understand its roles, regulation, and mechanisms of action.This chapter describes the use of a tandem affinity purification approach followed by mass spectrometry analysis to try to identify and characterize the proteins involved in protein complexes in Arabidopsis thaliana and decipher some mechanisms of regulation of the modules. Important elements to consider in such an approach are first extensively exposed in the introduction. This technique, in combination with complementary approaches like yeast two-hybrid and bimolecular fluorescence complementation, can be an interesting source of data to identify and characterize in vivo protein complexes.
Collapse
Affiliation(s)
- Jean Bigeard
- URGV Plant Genomics, UMR INRA-1165/CNRS-ERL8196/Université d'Evry Val d'Essonne, 2, rue Gaston Crémieux, CP5708, 91057, Evry Cedex, France
| | | | | | | | | | | |
Collapse
|
41
|
Tandem affinity purification to identify cytosolic and nuclear gβγ-interacting proteins. Methods Mol Biol 2015; 1234:161-84. [PMID: 25304356 DOI: 10.1007/978-1-4939-1755-6_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
It has become clear in recent years that the Gβγ subunits of heterotrimeric proteins serve broad roles in the regulation of cellular activity and interact with many proteins in different subcellular locations including the nucleus. Protein affinity purification is a common method to identify and confirm protein interactions. When used in conjugation with mass spectrometry it can be used to identify novel protein interactions with a given bait protein. The tandem affinity purification (TAP) technique identifies partner proteins bound to tagged protein bait. Combined with protocols to enrich the nuclear fraction of whole cell lysate through sucrose cushions, TAP allows for purification of interacting proteins found specifically in the nucleus. Here we describe the use of the TAP technique on cytosolic and nuclear lysates to identify candidate proteins, through mass spectrometry, that bind to Gβ1 subunits.
Collapse
|
42
|
A mass spectrometry view of stable and transient protein interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:263-82. [PMID: 24952186 DOI: 10.1007/978-3-319-06068-2_11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Through an impressive range of dynamic interactions, proteins succeed to carry out the majority of functions in a cell. These temporally and spatially regulated interactions provide the means through which one single protein can perform diverse functions and modulate different cellular pathways. Understanding the identity and nature of these interactions is therefore critical for defining protein functions and their contribution to health and disease processes. Here, we provide an overview of workflows that incorporate immunoaffinity purifications and quantitative mass spectrometry (frequently abbreviated as IP-MS or AP-MS) for characterizing protein-protein interactions. We discuss experimental aspects that should be considered when optimizing the isolation of a protein complex. As the presence of nonspecific associations is a concern in these experiments, we discuss the common sources of nonspecific interactions and present label-free and metabolic labeling mass spectrometry-based methods that can help determine the specificity of interactions. The effective regulation of cellular pathways and the rapid reaction to various environmental stresses rely on the formation of stable, transient, and fast-exchanging protein-protein interactions. While determining the exact nature of an interaction remains challenging, we review cross-linking and metabolic labeling approaches that can help address this important aspect of characterizing protein interactions and macromolecular assemblies.
Collapse
|
43
|
Miladi B, Dridi C, El Marjou A, Boeuf G, Bouallagui H, Dufour F, Di Martino P, Elm'selmi A. An improved strategy for easy process monitoring and advanced purification of recombinant proteins. Mol Biotechnol 2014; 55:227-35. [PMID: 23780701 DOI: 10.1007/s12033-013-9673-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this work, a multifunctional expression cassette, termed Multitags, combining different and complementary functionalities, was designed and used to monitor the expression and the purification of two model proteins (Pfu DNA polymerase and Myosin-VIIa- and Rab-Interracting protein : MyRIP). Multitags contains two affinity purification tags, a polyhistidine sequence (10× His) and the streptavidin-binding peptide (SBP) and as a marker tag the heme-binding domain of rat cytochrome b5 followed by the TEV cleavage site. Using the Multitags as fusion partner, more than 90 % of both fusion proteins were produced in soluble form when expressed in Escherichia coli KRX. In addition, high purity (99 %) of recombinant proteins was achieved after two consecutive affinity purification steps. The expression cassette also demonstrated an accurate monitoring capability comparable to that of a dual recognition-based method. The choice of the SBP tag was considered as an integral process that included a method for tag removal. Thus, an immobilized TEV protease fixed on streptavidin-agarose matrix was used for the cleavage of fusion proteins. After digestion, both unprocessed fusion proteins and Multitags were retained on the proteolytic column via their SBP sequence, allowing cleavage and recovery of target proteins on one step. This combined approach may accelerate the development of optimized production processes, while insuring high product quality and a low production cost.
Collapse
Affiliation(s)
- Baligh Miladi
- Laboratoire de Biologie Moléculaire, Ecole de Biologie Industrielle, 32 Boulevard du port, 95094, Cergy-Pontoise cedex, France
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Wållberg H, Ståhl S. Design and evaluation of radiolabeled tracers for tumor imaging. Biotechnol Appl Biochem 2014; 60:365-83. [PMID: 24033592 DOI: 10.1002/bab.1111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/20/2013] [Indexed: 12/22/2022]
Abstract
The growing understanding of tumor biology and the identification of tumor-specific genetic and molecular alterations, such as the overexpression of membrane receptors and other proteins, allows for personalization of patient management using targeted therapies. However, this puts stringent demands on the diagnostic tools used to identify patients who are likely to respond to a particular treatment. Radionuclide molecular imaging is a promising noninvasive method to visualize and characterize the expression of such targets. A number of different proteins, from full-length antibodies and their derivatives to small scaffold proteins and peptide receptor-ligands, have been applied to molecular imaging, each demonstrating strengths and weaknesses. Here, we discuss the concept of molecular targeting and, in particular, molecular imaging of cancer-associated targets. Additionally, we describe important biotechnological considerations and desired features when designing and developing tracers for radionuclide molecular imaging.
Collapse
Affiliation(s)
- Helena Wållberg
- Division of Molecular Biotechnology, School of Biotechnology, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | | |
Collapse
|
45
|
Wood DW. New trends and affinity tag designs for recombinant protein purification. Curr Opin Struct Biol 2014; 26:54-61. [DOI: 10.1016/j.sbi.2014.04.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 01/14/2023]
|
46
|
Costa S, Almeida A, Castro A, Domingues L. Fusion tags for protein solubility, purification and immunogenicity in Escherichia coli: the novel Fh8 system. Front Microbiol 2014. [PMID: 24600443 DOI: 10.3389/fmicb.2014.00063.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins are now widely produced in diverse microbial cell factories. The Escherichia coli is still the dominant host for recombinant protein production but, as a bacterial cell, it also has its issues: the aggregation of foreign proteins into insoluble inclusion bodies is perhaps the main limiting factor of the E. coli expression system. Conversely, E. coli benefits of cost, ease of use and scale make it essential to design new approaches directed for improved recombinant protein production in this host cell. With the aid of genetic and protein engineering novel tailored-made strategies can be designed to suit user or process requirements. Gene fusion technology has been widely used for the improvement of soluble protein production and/or purification in E. coli, and for increasing peptide's immunogenicity as well. New fusion partners are constantly emerging and complementing the traditional solutions, as for instance, the Fh8 fusion tag that has been recently studied and ranked among the best solubility enhancer partners. In this review, we provide an overview of current strategies to improve recombinant protein production in E. coli, including the key factors for successful protein production, highlighting soluble protein production, and a comprehensive summary of the latest available and traditionally used gene fusion technologies. A special emphasis is given to the recently discovered Fh8 fusion system that can be used for soluble protein production, purification, and immunogenicity in E. coli. The number of existing fusion tags will probably increase in the next few years, and efforts should be taken to better understand how fusion tags act in E. coli. This knowledge will undoubtedly drive the development of new tailored-made tools for protein production in this bacterial system.
Collapse
Affiliation(s)
- Sofia Costa
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho Braga, Portugal ; Instituto Nacional de Saúde Dr. Ricardo Jorge Porto, Portugal
| | - André Almeida
- Hitag Biotechnology, Lad., Biocant, Parque Technologico de Cantanhede Cantanhede, Portugal
| | - António Castro
- Instituto Nacional de Saúde Dr. Ricardo Jorge Porto, Portugal
| | - Lucília Domingues
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho Braga, Portugal
| |
Collapse
|
47
|
Pina AS, Lowe CR, Roque ACA. Challenges and opportunities in the purification of recombinant tagged proteins. Biotechnol Adv 2014; 32:366-81. [PMID: 24334194 PMCID: PMC7125906 DOI: 10.1016/j.biotechadv.2013.12.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/04/2013] [Accepted: 12/08/2013] [Indexed: 01/05/2023]
Abstract
The purification of recombinant proteins by affinity chromatography is one of the most efficient strategies due to the high recovery yields and purity achieved. However, this is dependent on the availability of specific affinity adsorbents for each particular target protein. The diversity of proteins to be purified augments the complexity and number of specific affinity adsorbents needed, and therefore generic platforms for the purification of recombinant proteins are appealing strategies. This justifies why genetically encoded affinity tags became so popular for recombinant protein purification, as these systems only require specific ligands for the capture of the fusion protein through a pre-defined affinity tag tail. There is a wide range of available affinity pairs "tag-ligand" combining biological or structural affinity ligands with the respective binding tags. This review gives a general overview of the well-established "tag-ligand" systems available for fusion protein purification and also explores current unconventional strategies under development.
Collapse
Affiliation(s)
- Ana Sofia Pina
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; IBET-Instituto de Biologia Experimental Tecnológica, Oeiras, Portugal
| | - Christopher R Lowe
- Institute of Biotechnology, Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, CB2 1QT Cambridge, UK
| | - Ana Cecília A Roque
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| |
Collapse
|
48
|
Costa S, Almeida A, Castro A, Domingues L. Fusion tags for protein solubility, purification and immunogenicity in Escherichia coli: the novel Fh8 system. Front Microbiol 2014; 5:63. [PMID: 24600443 PMCID: PMC3928792 DOI: 10.3389/fmicb.2014.00063] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/30/2014] [Indexed: 01/19/2023] Open
Abstract
Proteins are now widely produced in diverse microbial cell factories. The Escherichia coli is still the dominant host for recombinant protein production but, as a bacterial cell, it also has its issues: the aggregation of foreign proteins into insoluble inclusion bodies is perhaps the main limiting factor of the E. coli expression system. Conversely, E. coli benefits of cost, ease of use and scale make it essential to design new approaches directed for improved recombinant protein production in this host cell. With the aid of genetic and protein engineering novel tailored-made strategies can be designed to suit user or process requirements. Gene fusion technology has been widely used for the improvement of soluble protein production and/or purification in E. coli, and for increasing peptide's immunogenicity as well. New fusion partners are constantly emerging and complementing the traditional solutions, as for instance, the Fh8 fusion tag that has been recently studied and ranked among the best solubility enhancer partners. In this review, we provide an overview of current strategies to improve recombinant protein production in E. coli, including the key factors for successful protein production, highlighting soluble protein production, and a comprehensive summary of the latest available and traditionally used gene fusion technologies. A special emphasis is given to the recently discovered Fh8 fusion system that can be used for soluble protein production, purification, and immunogenicity in E. coli. The number of existing fusion tags will probably increase in the next few years, and efforts should be taken to better understand how fusion tags act in E. coli. This knowledge will undoubtedly drive the development of new tailored-made tools for protein production in this bacterial system.
Collapse
Affiliation(s)
- Sofia Costa
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho Braga, Portugal ; Instituto Nacional de Saúde Dr. Ricardo Jorge Porto, Portugal
| | - André Almeida
- Hitag Biotechnology, Lad., Biocant, Parque Technologico de Cantanhede Cantanhede, Portugal
| | - António Castro
- Instituto Nacional de Saúde Dr. Ricardo Jorge Porto, Portugal
| | - Lucília Domingues
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho Braga, Portugal
| |
Collapse
|
49
|
Yoshimatsu K, Yamazaki T, Hoshino Y, Rose PE, Epstein LF, Miranda LP, Tagari P, Beierle JM, Yonamine Y, Shea KJ. Epitope discovery for a synthetic polymer nanoparticle: a new strategy for developing a peptide tag. J Am Chem Soc 2014; 136:1194-7. [PMID: 24410250 PMCID: PMC3985795 DOI: 10.1021/ja410817p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
We describe a novel epitope discovery
strategy for creating an
affinity agent/peptide tag pair. A synthetic polymer nanoparticle
(NP) was used as the “bait” to catch an affinity peptide
tag. Biotinylated peptide tag candidates of varied sequence and length
were attached to an avidin platform and screened for affinity against
the polymer NP. NP affinity for the avidin/peptide tag complexes was
used to provide insight into factors that contribute NP/tag binding.
The identified epitope sequence with an optimized length (tMel-tag)
was fused to two recombinant proteins. The tagged proteins exhibited
higher NP affinity than proteins without tags. The results establish
that a fusion peptide tag consisting of optimized 15 amino acid residues
can provide strong affinity to an abiotic polymer NP. The affinity
and selectivity of NP/tMel-tag interactions were exploited for protein
purification in conjunction with immobilized metal ion/His6-tag interactions
to prepare highly purified recombinant proteins. This strategy makes
available inexpensive, abiotic synthetic polymers as affinity agents
for peptide tags and provides alternatives for important applications
where more costly affinity agents are used.
Collapse
Affiliation(s)
- Keiichi Yoshimatsu
- Department of Chemistry, University of California , Irvine, California 92697, United States
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Several affinity tags commonly used in chromatographic purification. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2013; 2013:581093. [PMID: 24490106 PMCID: PMC3893739 DOI: 10.1155/2013/581093] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/11/2013] [Accepted: 12/02/2013] [Indexed: 02/05/2023]
Abstract
Affinity tags have become powerful tools from basic biological research to structural and functional proteomics. They were widely used to facilitate the purification and detection of proteins of interest, as well as the separation of protein complexes. Here, we mainly discuss the benefits and drawbacks of several affinity or epitope tags frequently used, including hexahistidine tag, FLAG tag, Strep II tag, streptavidin-binding peptide (SBP) tag, calmodulin-binding peptide (CBP), glutathione S-transferase (GST), maltose-binding protein (MBP), S-tag, HA tag, and c-Myc tag. In some cases, a large-size affinity tag, such as GST or MBP, can significantly impact on the structure and biological activity of the fusion partner protein. So it is usually necessary to excise the tag by protease. The most commonly used endopeptidases are enterokinase, factor Xa, thrombin, tobacco etch virus, and human rhinovirus 3C protease. The proteolysis features of these proteases are described in order to provide a general guidance on the proteolytic removal of the affinity tags.
Collapse
|