1
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Huo Y, Li H, Wang X, Du X, Swain PS. Nunchaku: optimally partitioning data into piece-wise contiguous segments. Bioinformatics 2023; 39:btad688. [PMID: 37966918 PMCID: PMC10697733 DOI: 10.1093/bioinformatics/btad688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023] Open
Abstract
MOTIVATION When analyzing 1D time series, scientists are often interested in identifying regions where one variable depends linearly on the other. Typically, they use an ad hoc and therefore often subjective method to do so. RESULTS Here, we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a dataset not only into contiguous piece-wise linear segments, but also into contiguous segments described by linear combinations of arbitrary basis functions. We therefore present a general solution to the problem of identifying discontinuous change points. Focusing on microbial growth, we use the algorithm to find the range of optical density where this density is linearly proportional to the number of cells and to automatically find the regions of exponential growth for both Escherichia coli and Saccharomyces cerevisiae. For budding yeast, we consequently are able to infer the Monod constant for growth on fructose. Our algorithm lends itself to automation and high throughput studies, increases reproducibility, and should facilitate data analyses for a broad range of scientists. AVAILABILITY AND IMPLEMENTATION The corresponding Python package, entitled Nunchaku, is available at PyPI: https://pypi.org/project/nunchaku.
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Affiliation(s)
- Yu Huo
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Hongpei Li
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Xiao Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Xiaochen Du
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Peter S Swain
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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2
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Gidden Z, Oi C, Johnston EJ, Konieczna Z, Bhaskar H, Mendive-Tapia L, de Moliner F, Rosser SJ, Mochrie SGJ, Vendrell M, Horrocks MH, Regan L. Imaging Proteins Sensitive to Direct Fusions Using Transient Peptide-Peptide Interactions. NANO LETTERS 2023; 23:10633-10641. [PMID: 37916770 PMCID: PMC10683072 DOI: 10.1021/acs.nanolett.3c03780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023]
Abstract
Fluorescence microscopy enables specific visualization of proteins in living cells and has played an important role in our understanding of the protein subcellular location and function. Some proteins, however, show altered localization or function when labeled using direct fusions to fluorescent proteins, making them difficult to study in live cells. Additionally, the resolution of fluorescence microscopy is limited to ∼200 nm, which is 2 orders of magnitude larger than the size of most proteins. To circumvent these challenges, we previously developed LIVE-PAINT, a live-cell super-resolution approach that takes advantage of short interacting peptides to transiently bind a fluorescent protein to the protein-of-interest. Here, we successfully use LIVE-PAINT to image yeast membrane proteins that do not tolerate the direct fusion of a fluorescent protein by using peptide tags as short as 5-residues. We also demonstrate that it is possible to resolve multiple proteins at the nanoscale concurrently using orthogonal peptide interaction pairs.
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Affiliation(s)
- Zoe Gidden
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- EaStCHEM
School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, U.K.
| | - Curran Oi
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Emily J. Johnston
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- Centre
for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
| | - Zuzanna Konieczna
- EaStCHEM
School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, U.K.
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Haresh Bhaskar
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- EaStCHEM
School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, U.K.
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Lorena Mendive-Tapia
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
- Centre
for
Inflammation Research, The University of
Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Fabio de Moliner
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
- Centre
for
Inflammation Research, The University of
Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Susan J. Rosser
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- Centre
for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
| | - Simon G. J. Mochrie
- Department
of Physics, Yale University, New Haven, Connecticut 06520, United States
- Integrated
Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Marc Vendrell
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
- Centre
for
Inflammation Research, The University of
Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Mathew H. Horrocks
- EaStCHEM
School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, U.K.
- IRR
Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, U.K.
| | - Lynne Regan
- School
of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, U.K.
- Centre
for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, U.K.
- Integrated
Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, United States
- Institute
of Quantitative Biology, Biochemistry and Biotechnology, Edinburgh, EH9 3FF, U.K.
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3
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Bailey MLP, Pratt SE, Hinrichsen M, Zhang Y, Bewersdorf J, Regan LJ, Mochrie SGJ. Uncovering diffusive states of the yeast membrane protein, Pma1, and how labeling method can change diffusive behavior. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:42. [PMID: 37294385 PMCID: PMC10369454 DOI: 10.1140/epje/s10189-023-00301-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
We present and analyze video-microscopy-based single-particle-tracking measurements of the budding yeast (Saccharomyces cerevisiae) membrane protein, Pma1, fluorescently labeled either by direct fusion to the switchable fluorescent protein, mEos3.2, or by a novel, light-touch, labeling scheme, in which a 5 amino acid tag is directly fused to the C-terminus of Pma1, which then binds mEos3.2. The track diffusivity distributions of these two populations of single-particle tracks differ significantly, demonstrating that labeling method can be an important determinant of diffusive behavior. We also applied perturbation expectation maximization (pEMv2) (Koo and Mochrie in Phys Rev E 94(5):052412, 2016), which sorts trajectories into the statistically optimum number of diffusive states. For both TRAP-labeled Pma1 and Pma1-mEos3.2, pEMv2 sorts the tracks into two diffusive states: an essentially immobile state and a more mobile state. However, the mobile fraction of Pma1-mEos3.2 tracks is much smaller ([Formula: see text]) than the mobile fraction of TRAP-labeled Pma1 tracks ([Formula: see text]). In addition, the diffusivity of Pma1-mEos3.2's mobile state is several times smaller than the diffusivity of TRAP-labeled Pma1's mobile state. Thus, the two different labeling methods give rise to very different overall diffusive behaviors. To critically assess pEMv2's performance, we compare the diffusivity and covariance distributions of the experimental pEMv2-sorted populations to corresponding theoretical distributions, assuming that Pma1 displacements realize a Gaussian random process. The experiment-theory comparisons for both the TRAP-labeled Pma1 and Pma1-mEos3.2 reveal good agreement, bolstering the pEMv2 approach.
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Affiliation(s)
- Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA
| | - Susan E Pratt
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
| | | | - Yongdeng Zhang
- Department of Cell Biology, Yale University, New Haven, CT, 06511, USA
| | - Joerg Bewersdorf
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
- Department of Cell Biology, Yale University, New Haven, CT, 06511, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
| | - Lynne J Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, 06511, UK
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA.
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA.
- Department of Physics, Yale University, New Haven, CT, 06511, USA.
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4
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Oi C, Mochrie SGJ, Horrocks MH, Regan L. PAINT using proteins: A new brush for super-resolution artists. Protein Sci 2020; 29:2142-2149. [PMID: 32949055 PMCID: PMC7586915 DOI: 10.1002/pro.3953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023]
Abstract
PAINT (points accumulation for imaging in nanoscale topography) refers to methods that achieve the sparse temporal labeling required for super-resolution imaging by using transient interactions between a biomolecule of interest and a fluorophore. There have been a variety of different implementations of this method since it was first described in 2006. Recent papers illustrate how transient peptide-protein interactions, rather than small molecule binding or DNA oligonucleotide duplex formation, can be employed to perform PAINT-based single molecule localization microscopy (SMLM). We discuss the different approaches to PAINT using peptide and protein interactions, and their applications in vitro and in vivo. We highlight the important parameters to consider when selecting suitable peptide-protein interaction pairs for such studies. We also note the opportunities for protein scientists to apply their expertise in guiding the choice of peptide and protein pairs that are used. Finally, we discuss the potential for expanding super-resolution imaging methods based on transient peptide-protein interactions, including the development of simultaneous multicolor imaging of multiple proteins and the study of very high and very low abundance proteins in live cells.
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Affiliation(s)
- Curran Oi
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenConnecticutUSA
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
| | - Simon G. J. Mochrie
- Integrated Graduate Program in Physical and Engineering BiologyYale UniversityNew HavenConnecticutUSA
- Department of PhysicsYale UniversityNew HavenConnecticutUSA
| | | | - Lynne Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Centre for Synthetic and Systems Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
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5
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Cleveland JD, Tucker CL. Photo-SNAP-tag, a Light-Regulated Chemical Labeling System. ACS Chem Biol 2020; 15:2212-2220. [PMID: 32623878 DOI: 10.1021/acschembio.0c00412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods that allow labeling and tracking of proteins have been instrumental for understanding their function. Traditional methods for labeling proteins include fusion to fluorescent proteins or self-labeling chemical tagging systems such as SNAP-tag or Halo-tag. These latter approaches allow bright fluorophores or other chemical moieties to be attached to a protein of interest through a small fusion tag. In this work, we sought to improve the versatility of self-labeling chemical-tagging systems by regulating their activity with light. We used light-inducible dimerizers to reconstitute a split SNAP-tag (modified human O6-alkylguanine-DNA-alkyltransferase, hAGT) protein, allowing tight light-dependent control of chemical labeling. In addition, we generated a small split SNAP-tag fragment that can efficiently self-assemble with its complement fragment, allowing high labeling efficacy with a small tag. We envision these tools will extend the versatility and utility of the SNAP-tag chemical system for protein labeling applications.
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Affiliation(s)
- Joseph D. Cleveland
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
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6
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Oi C, Gidden Z, Holyoake L, Kantelberg O, Mochrie S, Horrocks MH, Regan L. LIVE-PAINT allows super-resolution microscopy inside living cells using reversible peptide-protein interactions. Commun Biol 2020; 3:458. [PMID: 32820217 PMCID: PMC7441314 DOI: 10.1038/s42003-020-01188-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 11/09/2022] Open
Abstract
We present LIVE-PAINT, a new approach to super-resolution fluorescent imaging inside live cells. In LIVE-PAINT only a short peptide sequence is fused to the protein being studied, unlike conventional super-resolution methods, which rely on directly fusing the biomolecule of interest to a large fluorescent protein, organic fluorophore, or oligonucleotide. LIVE-PAINT works by observing the blinking of localized fluorescence as this peptide is reversibly bound by a protein that is fused to a fluorescent protein. We have demonstrated the effectiveness of LIVE-PAINT by imaging a number of different proteins inside live S. cerevisiae. Not only is LIVE-PAINT widely applicable, easily implemented, and the modifications minimally perturbing, but we also anticipate it will extend data acquisition times compared to those previously possible with methods that involve direct fusion to a fluorescent protein.
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Affiliation(s)
- Curran Oi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
| | - Zoe Gidden
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, Scotland
| | - Louise Holyoake
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, Scotland
| | - Owen Kantelberg
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, Scotland
| | - Simon Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
- Department of Physics, Yale University, New Haven, CT, 06520, USA
| | - Mathew H Horrocks
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, Scotland.
| | - Lynne Regan
- Center for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, Scotland.
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7
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Keeble AH, Howarth M. Power to the protein: enhancing and combining activities using the Spy toolbox. Chem Sci 2020; 11:7281-7291. [PMID: 33552459 PMCID: PMC7844731 DOI: 10.1039/d0sc01878c] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Proteins span an extraordinary range of shapes, sizes and functionalities. Therefore generic approaches are needed to overcome this diversity and stream-line protein analysis or application. Here we review SpyTag technology, now used in hundreds of publications or patents, and its potential for detecting and controlling protein behaviour. SpyTag forms a spontaneous and irreversible isopeptide bond upon binding its protein partner SpyCatcher, where both parts are genetically-encoded. New variants of this pair allow reaction at a rate approaching the diffusion limit, while reversible versions allow purification of SpyTagged proteins or tuned dynamic interaction inside cells. Anchoring of SpyTag-linked proteins has been established to diverse nanoparticles or surfaces, including gold, graphene and the air/water interface. SpyTag/SpyCatcher is mechanically stable, so is widely used for investigating protein folding and force sensitivity. A toolbox of scaffolds allows SpyTag-fusions to be assembled into defined multimers, from dimers to 180-mers, or unlimited 1D, 2D or 3D networks. Icosahedral multimers are being evaluated for vaccination against malaria, HIV and cancer. For enzymes, Spy technology has increased resilience, promoted substrate channelling, and assembled hydrogels for continuous flow biocatalysis. Combinatorial increase in functionality has been achieved through modular derivatisation of antibodies, light-emitting diodes or viral vectors. In living cells, SpyTag allowed imaging of protein trafficking, retargeting of CAR-T cell killing, investigation of heart contraction, and control of nucleosome position. The simple genetic encoding and rapid irreversible reaction provide diverse opportunities to enhance protein function. We describe limitations as well as future directions.
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Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
| | - Mark Howarth
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford , OX1 3QU , UK . ; Tel: +44 (0)1865 613200
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8
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Zhang N, Liu J, Liu Y, Wu WH, Fang J, Da XD, Wang S, Zhang WB. NMR Spectroscopic Studies Reveal the Critical Role of the Isopeptide Bond in Forming the Otherwise Unstable SpyTag-SpyCatcher Mutant Complexes. Biochemistry 2020; 59:2226-2236. [PMID: 32469203 DOI: 10.1021/acs.biochem.0c00287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interplay between protein folding and chemical reaction has been an intriguing subject. In this contribution, we report the study of SpyTag and SpyCatcher reactive mutants using a combination of sodium dodecyl sulfate-polyacrylamide gel electrophoresis, liquid chromatography and mass spectrometry, circular dichroism, and NMR spectroscopy. It was found that the wild-type SpyCatcher is well-folded in solution and docks with SpyTag to form an intermediate that promotes isopeptide bond formation. By contrast, the double mutant SpyCatcherVA is disordered in solution yet remains reactive toward SpyTag, forming a well-folded covalent complex. Control experiments using the catalytically inactive mutants further reveal the critical role of the isopeptide bond in stabilizing the otherwise loose SpyTag-SpyCatcherVA complex, amplifying the effect of the minute sequence disparity. We believe that the synergy between protein folding and isopeptide bonding is an effective way to enhance protein stability and engineer protein-protein interactions.
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Affiliation(s)
- Nan Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Jing Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Beijing NMR Center, Peking University, Beijing 100871, P. R. China
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Xiao-Di Da
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
| | - Shenlin Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Beijing NMR Center, Peking University, Beijing 100871, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.,Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, Peking University, Beijing 100871, P. R. China
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9
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Xu J, Kato T, Park EY. Development of SpyTag/SpyCatcher-Bacmid Expression Vector System (SpyBEVS) for Protein Bioconjugations Inside of Silkworms. Int J Mol Sci 2019; 20:ijms20174228. [PMID: 31470538 PMCID: PMC6747175 DOI: 10.3390/ijms20174228] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022] Open
Abstract
Protein conjugations at post-translational levels are known to be essential to protein stability and function. Recently, it has been proven that the split protein CnaB2 (SpyTag/SpyCatcher, ST/SC) from Streptococcus pyogenes can induce covalent conjugation rapidly and efficiently under various conditions. The protein of interest fused with the split protein SC/ST could be assembled spontaneously. In light of this finding, we introduced the ST/SC protein coupling concept into the silkworm-bacmid protein expression system (SpyBEVS). As a proof of concept, we first examined and confirmed that a competent ligation occurred between ST/SC-fused protein partners in vitro in cultured silkworm cells and in vivo in silkworm larvae by co-infection of several recombinant baculoviruses. The protein conjugation could be also achieved sufficiently by a simple one-step mixture of purified ST/SC-tagged peptide-protein pairs in vitro. Given the flexibility and robustness of silkworm-BEVS, our results on SpyBEVS show an alternative method for enabling the production of protein decorations in vitro and inside of silkworms.
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Affiliation(s)
- Jian Xu
- Laboratory of Biotechnology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Tatsuya Kato
- Laboratory of Biotechnology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Laboratory of Biotechnology, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Laboratory of Biotechnology, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Enoch Y Park
- Laboratory of Biotechnology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
- Laboratory of Biotechnology, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
- Laboratory of Biotechnology, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
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10
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Hatlem D, Trunk T, Linke D, Leo JC. Catching a SPY: Using the SpyCatcher-SpyTag and Related Systems for Labeling and Localizing Bacterial Proteins. Int J Mol Sci 2019; 20:E2129. [PMID: 31052154 PMCID: PMC6539128 DOI: 10.3390/ijms20092129] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/05/2023] Open
Abstract
The SpyCatcher-SpyTag system was developed seven years ago as a method for protein ligation. It is based on a modified domain from a Streptococcus pyogenes surface protein (SpyCatcher), which recognizes a cognate 13-amino-acid peptide (SpyTag). Upon recognition, the two form a covalent isopeptide bond between the side chains of a lysine in SpyCatcher and an aspartate in SpyTag. This technology has been used, among other applications, to create covalently stabilized multi-protein complexes, for modular vaccine production, and to label proteins (e.g., for microscopy). The SpyTag system is versatile as the tag is a short, unfolded peptide that can be genetically fused to exposed positions in target proteins; similarly, SpyCatcher can be fused to reporter proteins such as GFP, and to epitope or purification tags. Additionally, an orthogonal system called SnoopTag-SnoopCatcher has been developed from an S. pneumoniae pilin that can be combined with SpyCatcher-SpyTag to produce protein fusions with multiple components. Furthermore, tripartite applications have been produced from both systems allowing the fusion of two peptides by a separate, catalytically active protein unit, SpyLigase or SnoopLigase. Here, we review the current state of the SpyCatcher-SpyTag and related technologies, with a particular emphasis on their use in vaccine development and in determining outer membrane protein localization and topology of surface proteins in bacteria.
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Affiliation(s)
- Daniel Hatlem
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Thomas Trunk
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Dirk Linke
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Jack C Leo
- Bacterial Cell Surface Group, Section for Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
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11
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Insider information on successful covalent protein coupling with help from SpyBank. Methods Enzymol 2019; 617:443-461. [DOI: 10.1016/bs.mie.2018.12.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Zhang XJ, Wu XL, Liu D, Da XD, Wang XW, Yang S, Zhang WB. Engineering SpyCatcher Variants with Proteolytic Sites for Less-Trace Ligation. CHINESE J CHEM 2018. [DOI: 10.1002/cjoc.201800475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xue-Jian Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University; Shanghai 201620 China
| | - Xia-Ling Wu
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University; Beijing 100871 China
| | - Dong Liu
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University; Beijing 100871 China
| | - Xiao-Di Da
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University; Beijing 100871 China
| | - Xiao-Wei Wang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University; Beijing 100871 China
| | - Shuguang Yang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-dimension Materials, College of Material Science and Engineering, Donghua University; Shanghai 201620 China
| | - Wen-Bin Zhang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University; Beijing 100871 China
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Wu XL, Liu Y, Liu D, Sun F, Zhang WB. An Intrinsically Disordered Peptide-Peptide Stapler for Highly Efficient Protein Ligation Both in Vivo and in Vitro. J Am Chem Soc 2018; 140:17474-17483. [PMID: 30449090 DOI: 10.1021/jacs.8b08250] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein, we report an intrinsically disordered protein SpyStapler that can catalyze the isopeptide bond formation between two peptide tags, that is, SpyTag and BDTag, both in vitro and in vivo. SpyStapler and BDTag are developed by splitting SpyCatcher-the cognate protein partner of SpyTag-at the more solvent exposed second loop region. Regardless of their locations in protein constructs, SpyStapler enables efficient covalent coupling of SpyTag and BDTag under a variety of mild conditions in vitro (yield ∼80%). Co-expression of SpyStapler with telechelic dihydrofolate reductase (DHFR) bearing a SpyTag at N-terminus and a BDTag at C-terminus leads to direct cellular synthesis of a circular DHFR. Mechanistic studies involving circular dichroism and nuclear magnetic resonance spectrometry reveal that SpyStapler alone is disordered in solution and forms a stable folded structure ( Tm ∼ 55 °C) in the presence of both SpyTag and BDTag upon isopeptide bonding. No ordered structure can be formed in the absence of either tag. The catalytically inactive SpyStapler-EQ mutant cannot form a stable physical complex with SpyTag and BDTag, but it can fold into ordered structure in the presence of the ligated product (SpyTag-BDTag). It suggests that the isopeptide bond is important in stabilizing the complex. Given its efficiency, resilience, and robustness, SpyStapler provides new opportunities for bioconjugation and creation of complex protein architectures.
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Affiliation(s)
- Xia-Ling Wu
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Yajie Liu
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Dong Liu
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Fei Sun
- Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong SAR , P. R. China
| | - Wen-Bin Zhang
- Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
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14
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Brune KD, Howarth M. New Routes and Opportunities for Modular Construction of Particulate Vaccines: Stick, Click, and Glue. Front Immunol 2018; 9:1432. [PMID: 29997617 PMCID: PMC6028521 DOI: 10.3389/fimmu.2018.01432] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 06/11/2018] [Indexed: 02/02/2023] Open
Abstract
Vaccines based on virus-like particles (VLPs) can induce potent B cell responses. Some non-chimeric VLP-based vaccines are highly successful licensed products (e.g., hepatitis B surface antigen VLPs as a hepatitis B virus vaccine). Chimeric VLPs are designed to take advantage of the VLP framework by decorating the VLP with a different antigen. Despite decades of effort, there have been few licensed chimeric VLP vaccines. Classic approaches to create chimeric VLPs are either genetic fusion or chemical conjugation, using cross-linkers from lysine on the VLP to cysteine on the antigen. We describe the principles that make these classic approaches challenging, in particular for complex, full-length antigens bearing multiple post-translational modifications. We then review recent advances in conjugation approaches for protein-based non-enveloped VLPs or nanoparticles, to overcome such challenges. This includes the use of strong non-covalent assembly methods (stick), unnatural amino acids for bio-orthogonal chemistry (click), and spontaneous isopeptide bond formation by SpyTag/SpyCatcher (glue). Existing applications of these methods are outlined and we critically consider the key practical issues, with particular insight on Tag/Catcher plug-and-display decoration. Finally, we highlight the potential for modular particle decoration to accelerate vaccine generation and prepare for pandemic threats in human and veterinary realms.
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Affiliation(s)
- Karl D Brune
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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15
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Ke X, Zhang Y, Zheng F, Liu Y, Zheng Z, Xu Y, Wang H. SpyCatcher-SpyTag mediated in situ labelling of progeny baculovirus with quantum dots for tracking viral infection in living cells. Chem Commun (Camb) 2018; 54:1189-1192. [PMID: 29334085 DOI: 10.1039/c7cc08880a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A non-invasive labelling strategy is proposed to label baculovirus via genetic insertion of a SpyTag into the viral glycoprotein, followed by specific conjugation with the SpyCatcher protein on modified quantum dots (QDs) through an isopeptide bond. The labelling method is convenient and efficient and shows little attenuation of viral infectivity. Therefore, it is a biologically compatible technique for tracking viral infection.
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Affiliation(s)
- Xianliang Ke
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
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