1
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Zhu Y. Improved elution strategy and new monoclonal anti-biotin antibody for LC-MS/MS characterization of protein biotinylation sites. Biochem Biophys Rep 2024; 38:101711. [PMID: 38681669 PMCID: PMC11052901 DOI: 10.1016/j.bbrep.2024.101711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
Biotin labeling in combination with mass spectrometry has been widely applied in large-scale biological studies, such as determination of protein partners, protein subcellular localization, and protein post-translational modifications. Previous studies have shown that immunoaffinity enrichment is a better method than streptavidin/avidin purification for site-specific studies of biotinylated molecules. In this study, we made a crucial improvement to the elution phase of the immunoaffinity enrichment step for biotinylated peptides, which involves the addition of a highly organic solvent, and developed a monoclonal anti-biotin antibody that improved the identification number for biotinylated peptides. We then demonstrated its application in the characterization of protein interaction sites for the β2 adrenergic receptor (β2AR) by proximity labeling in living cells. Our research provides an improved and reproducible immunoaffinity enrichment method for site-specific biotin-related research.
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Affiliation(s)
- Yiying Zhu
- Tsinghua University and Cell Signaling Technology Inc, Chemistry Department, Tsinghua University, Beijing, 100084, China
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2
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Enström A, Carlsson R, Buizza C, Lewi M, Paul G. Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular in Vitro Spheroid Model. Mol Cell Proteomics 2024; 23:100782. [PMID: 38705386 PMCID: PMC11176767 DOI: 10.1016/j.mcpro.2024.100782] [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] [Received: 08/22/2023] [Revised: 04/09/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024] Open
Abstract
Cellular communication within the brain is imperative for maintaining homeostasis and mounting effective responses to pathological triggers like hypoxia. However, a comprehensive understanding of the precise composition and dynamic release of secreted molecules has remained elusive, confined primarily to investigations using isolated monocultures. To overcome these limitations, we utilized the potential of TurboID, a non-toxic biotin ligation enzyme, to capture and enrich secreted proteins specifically originating from human brain pericytes in spheroid cocultures with human endothelial cells and astrocytes. This approach allowed us to characterize the pericyte secretome within a more physiologically relevant multicellular setting encompassing the constituents of the blood-brain barrier. Through a combination of mass spectrometry and multiplex immunoassays, we identified a wide spectrum of different secreted proteins by pericytes. Our findings demonstrate that the pericytes secretome is profoundly shaped by their intercellular communication with other blood-brain barrier-residing cells. Moreover, we identified substantial differences in the secretory profiles between hypoxic and normoxic pericytes. Mass spectrometry analysis showed that hypoxic pericytes in coculture increase their release of signals related to protein secretion, mTOR signaling, and the complement system, while hypoxic pericytes in monocultures showed an upregulation in proliferative pathways including G2M checkpoints, E2F-, and Myc-targets. In addition, hypoxic pericytes show an upregulation of proangiogenic proteins such as VEGFA but display downregulation of canonical proinflammatory cytokines such as CXCL1, MCP-1, and CXCL6. Understanding the specific composition of secreted proteins in the multicellular brain microvasculature is crucial for advancing our knowledge of brain homeostasis and the mechanisms underlying pathology. This study has implications for the identification of targeted therapeutic strategies aimed at modulating microvascular signaling in brain pathologies associated with hypoxia.
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Affiliation(s)
- Andreas Enström
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Robert Carlsson
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Carolina Buizza
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Marvel Lewi
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden
| | - Gesine Paul
- Translational Neurology Group, Department of Clinical Science, Lund University, Lund, Sweden; Department of Neurology, Scania University Hospital, Lund, Sweden; Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden.
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3
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Schreiber KJ, Kadijk E, Youn JY. Exploring Options for Proximity-Dependent Biotinylation Experiments: Comparative Analysis of Labeling Enzymes and Affinity Purification Resins. J Proteome Res 2024; 23:1531-1543. [PMID: 38507741 PMCID: PMC11002925 DOI: 10.1021/acs.jproteome.3c00908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Proximity-dependent biotinylation (PDB) techniques provide information about the molecular neighborhood of a protein of interest, yielding insights into its function and localization. Here, we assessed how different labeling enzymes and streptavidin resins influence PDB results. We compared the high-confidence interactors of the DNA/RNA-binding protein transactive response DNA-binding protein 43 kDa (TDP-43) identified using either miniTurbo (biotin ligase) or APEX2 (peroxidase) enzymes. We also evaluated two commercial affinity resins for purification of biotinylated proteins: conventional streptavidin sepharose versus a new trypsin-resistant streptavidin conjugated to magnetic resin, which significantly reduces the level of contamination by streptavidin peptides following on-bead trypsin digestion. Downstream analyses involved liquid chromatography coupled to mass spectrometry in data-dependent acquisition mode, database searching, and statistical analysis of high-confidence interactors using SAINTexpress. The APEX2-TDP-43 experiment identified more interactors than miniTurbo-TDP-43, although miniTurbo provided greater overlap with previously documented TDP-43 interactors. Purifications on sepharose resin yielded more interactors than magnetic resin in small-scale experiments using a range of magnetic resin volumes. We suggest that resin-specific background protein binding profiles and different lysate-to-resin ratios cumulatively affect the distributions of prey protein abundance in experimental and control samples, which impact statistical confidence scores. Overall, we highlight key experimental variables to consider for the empirical optimization of PDB experiments.
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Affiliation(s)
- Karl J. Schreiber
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Eileigh Kadijk
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ji-Young Youn
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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4
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Taggart EL, Wolff EJ, Yanar P, Blobe JP, Shugrue CR. Development of an oxazole-based cleavable linker for peptides. Bioorg Med Chem 2024; 102:117663. [PMID: 38457910 DOI: 10.1016/j.bmc.2024.117663] [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] [Received: 12/08/2023] [Revised: 02/06/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
We report the development of a new oxazole-based cleavable linker to release peptides from attached cargo. Oxazoles are stable to most reaction conditions, yet they can be rapidly cleaved in the presence of single-electron oxidants like cerium ammonium nitrate (CAN). An oxazole linker could be synthesized and attached to peptides through standard solid-phase peptide coupling reactions. Cleavage of these peptide-oxazole conjugates is demonstrated on a broad scope of peptides containing various natural and unnatural amino acids. These results represent the first example of a peptide-based linker that is cleaved through single-electron oxidation. The oxazole is also demonstrated to be a suitable linker for both the release of a peptide from a conjugated small molecule and the orthogonal release of cargo from a peptide containing multiple cleavable linkers. Oxazole linkers could serve as a promising tool for peptide screening platforms such as peptide-encoded libraries.
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Affiliation(s)
- Elizabeth L Taggart
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States
| | - Evan J Wolff
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States
| | - Pamira Yanar
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States
| | - John P Blobe
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States
| | - Christopher R Shugrue
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States.
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5
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Pleiko K, Haugas M, Parfejevs V, Pantelejevs T, Parisini E, Teesalu T, Riekstina U. Targeting triple-negative breast cancer cells with a β1-integrin binding aptamer. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:871-884. [PMID: 37680989 PMCID: PMC10481362 DOI: 10.1016/j.omtn.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/14/2023] [Indexed: 09/09/2023]
Abstract
Targeted therapies have increased the treatment options for triple-negative breast cancer patients. However, the paucity of targetable biomarkers and tumor heterogeneity have limited the ability of precision-guided interventions to live up to their full potential. As affinity-targeting ligands, aptamers show high selectivity toward target molecules. Compared with antibodies, aptamers have lower molecular weight, increased stability during transportation, reduced immunogenicity, and increased tissue uptake. Recently, we reported discovery of the GreenB1 aptamer, which is internalized in cultured triple-negative MDA-MB-231 human breast cancer cells. We show that the GreenB1 aptamer specifically targets β1-integrin, a protein linked previously to breast cancer cell invasiveness and migration. Aptamer binds to β1-integrin with low nanomolar affinity. Our findings suggest potential applications for GreenB1-guided precision agents for diagnosis and therapy of cancers overexpressing β1-integrin.
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Affiliation(s)
- Karlis Pleiko
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Maarja Haugas
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Vadims Parfejevs
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
| | | | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Tambet Teesalu
- Laboratory of Precision- and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
- Materials Research Laboratory, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Una Riekstina
- Faculty of Medicine, University of Latvia, House of Science, Jelgavas Str. 3, 1004 Riga, Latvia
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6
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Case KC, Beltman RJ, Pflum MKH, Greenberg ML. Valproate regulates inositol synthesis by reducing expression of myo-inositol-3-phosphate synthase. Sci Rep 2023; 13:14844. [PMID: 37684289 PMCID: PMC10491628 DOI: 10.1038/s41598-023-41936-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023] Open
Abstract
Inositol depletion is a hypothesized mechanism of action of mood stabilization drugs used in the treatment of bipolar disorder. It was previously reported that the mood stabilizer valproate (VPA) increased phosphorylation of myo-inositol-3-phosphate synthases (MIPS), the rate limiting enzyme of inositol synthesis. Phosphosites were identified and examination of site-directed mutants suggested that phosphorylation leads to decreased enzymatic activity. In this study, we examined the extent of MIPS phosphorylation in response to VPA and used two interaction screens to identify protein kinases that interact with MIPS. Using an epitope tagged MIPS construct, we determined the fraction of phosphorylated MIPS to be very low (less than 2% of total), and we could not detect phosphorylation of untagged MIPS in response to VPA. In vitro analyses of phosphorylation revealed that putative protein kinases, PKC and CKII, have low specificity toward MIPS. These findings suggest that VPA likely depletes inositol via a mechanism other than MIPS phosphorylation. Consistent with this, mRNA levels of the MIPS-encoding gene INO1 and MIPS protein levels were significantly reduced during the mid-log growth phase in response to VPA treatment. These findings suggest that the mechanism whereby VPA causes inositol depletion is by reducing expression of the rate-limiting enzyme MIPS.
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Affiliation(s)
- Kendall C Case
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Rachel J Beltman
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA.
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7
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Law D, Abdulkareem Najm A, Chong JX, K’ng JZY, Amran M, Ching HL, Wong RR, Leong MH, Mahdi IM, Fazry S. In silico identification and in vitro assessment of a potential anti-breast cancer activity of antimicrobial peptide retrieved from the ATMP1 Anabas testudineus fish peptide. PeerJ 2023; 11:e15651. [PMID: 37483971 PMCID: PMC10362845 DOI: 10.7717/peerj.15651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
A previous study has shown that synthetic antimicrobial peptides (AMPs) derived from Anabas testudineus (ATMP1) could in-vitro inhibit the progression of breast cancer cell lines. In this study, we are interested in studying altered versions of previous synthetic AMPs to gain some insight into the peptides functions. The AMPs were altered and subjected to bioinformatics prediction using four databases (ADP3, CAMP-R3, AMPfun, and ANTICP) to select the highest anticancer activity. The bioinformatics in silico analysis led to the selection of two AMPs, which are ATMP5 (THPPTTTTTTTTTTTYTAAPATTT) and ATMP6 (THPPTTTTTTTTTTTTTAAPARTT). The in silico analysis predicted that ATMP5 and ATMP6 have anticancer activity and lead to cell death. The ATMP5 and ATMP6 were submitted to deep learning databases (ToxIBTL and ToxinPred2) to predict the toxicity of the peptides and to (AllerTOP & AllergenFP) check the allergenicity. The results of databases indicated that AMPs are non-toxic to normal human cells and allergic to human immunoglobulin. The bioinformatics findings led to select the highest active peptide ATMP5, which was synthesised and applied for in-vitro experiments using cytotoxicity assay MTT Assay, apoptosis detection using the Annexin V FTIC-A assay, and gene expression using Apoptosis PCR Array to evaluate the AMP's anticancer activity. The antimicrobial activity is approved by the disc diffusion method. The in-vitro experiments analysis showed that ATMP5 had the activity to inhibit the growth of the breast cancer cell line (MDA-MB-231) after 48 h and managed to arrest the cell cycle of the MDA-MB-231, apoptosis induction, and overexpression of the p53 by interaction with the related apoptotic genes. This research opened up new opportunities for developing potential and selective anticancer agents relying on antimicrobial peptide properties.
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Affiliation(s)
- Douglas Law
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Ahmed Abdulkareem Najm
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Jia Xuan Chong
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Joelene Zi Ying K’ng
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Mas Amran
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Huey Lih Ching
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Rui Rui Wong
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - May Ho Leong
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Ibrahim Mahmood Mahdi
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Molecular Diagnostic Department, Karl Kolb GmBH & Co, KG, Dreieich, Germany
| | - Shazrul Fazry
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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8
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Kundu S, Jaiswal M, Craig KC, Guo J, Guo Z. Labeling cell surface glycosylphosphatidylinositol-anchored proteins through metabolic engineering using an azide-modified phosphatidylinositol. Biochem Biophys Res Commun 2023; 645:103-109. [PMID: 36682329 PMCID: PMC9899547 DOI: 10.1016/j.bbrc.2023.01.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/11/2023] [Indexed: 01/14/2023]
Abstract
Glycosylphosphatidylinositol (GPI) anchorage is one of the most common mechanisms to attach proteins to the plasma membrane of eukaryotic cells. GPI-anchored proteins (GPI-APs) play a critical role in many biological processes but are difficult to study. Here, a new method was developed for the effective and selective metabolic engineering and labeling of cell surface GPI-APs with an azide-modified phosphatidylinositol (PI) as the biosynthetic precursor of GPIs. It was demonstrated that this azido-PI derivative was taken up by HeLa cells and incorporated into the biosynthetic pathway of GPIs to present azide-labeled GPI-APs on the live cell surface. The azido group was used as a molecular handle to install other labels through a biocompatible click reaction to enable various biological studies, e.g., fluorescent imaging and protein pull-down, which can help explore the functions of GPI-APs and discover new GPI-APs.
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Affiliation(s)
| | | | | | | | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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9
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Zhai Y, Yu H, Liu X, Zhang M, Han R, Yin C, Liu X, Li H, Li J, Song X. Visual detection of Staphylococcus aureus based on immunomagnetic separation and polymerase spiral reaction. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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10
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Selective macrocyclic peptide modulators of Lys63-linked ubiquitin chains disrupt DNA damage repair. Nat Commun 2022; 13:6174. [PMID: 36257952 PMCID: PMC9579194 DOI: 10.1038/s41467-022-33808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Developing an effective binder for a specific ubiquitin (Ub) chain is a promising approach for modulating various biological processes with potential applications in drug discovery. Here, we combine the Random Non-standard Peptides Integrated Discovery (RaPID) method and chemical protein synthesis to screen an extended library of macrocyclic peptides against synthetic Lys63-linked Di-Ub to discover a specific binder for this Ub chain. Furthermore, next-generation binders are generated by chemical modifications. We show that our potent cyclic peptide is cell-permeable, and inhibits DNA damage repair, leading to apoptotic cell death. Concordantly, a pulldown experiment with the biotinylated analog of our lead cyclic peptide supports our findings. Collectively, we establish a powerful strategy for selective inhibition of protein-protein interactions associated with Lys63-linked Di-Ub using cyclic peptides. This study offers an advancement in modulating central Ub pathways and provides opportunities in drug discovery areas associated with Ub signaling.
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11
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Proximity labeling methods for proteomic analysis of membrane proteins. J Proteomics 2022; 264:104620. [DOI: 10.1016/j.jprot.2022.104620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022]
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12
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Tian X, Jiang H, Cai B, Feng H, Wang X, Yu G. Comparative Proteomic Analysis of Fucosylated Glycoproteins Produced by Bacteroides thetaiotaomicron Under Different Polysaccharide Nutrition Conditions. Front Microbiol 2022; 13:826942. [PMID: 35308349 PMCID: PMC8931616 DOI: 10.3389/fmicb.2022.826942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteroides thetaiotaomicron, one of the most eminent representative gut commensal Bacteroides species, is able to use the L-fucose in host-derived and dietary polysaccharides to modify its capsular polysaccharides and glycoproteins through a mammalian-like salvage metabolic pathway. This process is essential for the colonization of the bacteria and for symbiosis with the host. However, despite the importance of fucosylated proteins (FGPs) in B. thetaiotaomicron, their types, distribution, and functions remain unclear. In this study, the effects of different polysaccharide (corn starch, mucin, and fucoidan) nutrition conditions on newly synthesized FGPs expressions and fucosylation are investigated using a chemical biological method based on metabolic labeling and bioorthogonal reaction. According to the results of label-free quantification, 559 FGPs (205 downregulated and 354 upregulated) are affected by the dietary conditions. Of these differentially expressed proteins, 65 proteins show extremely sensitive to polysaccharide nutrition conditions (FGPs fold change/global protein fold change ≥2.0 or ≤0.5). Specifically, the fucosylation of the chondroitin sulfate ABC enzyme, Sus proteins, and cationic efflux system proteins varies significantly upon the addition of mucin, corn starch, or fucoidan. Moreover, these polysaccharides can trigger an appreciable increase in the fucosylation level of the two-component system and ammonium transport proteins. These results highlight the efficiency of the combined metabolic glycan labeling and bio-orthogonal reaction in enriching the intestinal Bacteroides glycoproteins. Moreover, it emphasizes the sensitivity of Bacteroides fucosylation to polysaccharide nutrition conditions, which allows for the regulation of bacterial growth.
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Affiliation(s)
- Xiao Tian
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Hao Jiang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Hao Jiang,
| | - Binbin Cai
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Huxin Feng
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Xuan Wang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Guangli Yu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Guangli Yu,
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13
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Najm AAK, Azfaralariff A, Dyari HRE, Othman BA, Shahid M, Khalili N, Law D, Syed Alwi SS, Fazry S. Anti-breast cancer synthetic peptides derived from the Anabas testudineus skin mucus fractions. Sci Rep 2021; 11:23182. [PMID: 34848729 PMCID: PMC8632885 DOI: 10.1038/s41598-021-02007-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/09/2021] [Indexed: 01/17/2023] Open
Abstract
Previous study has shown the antimicrobial activities of mucus protein extracted from Anabastestudineus. In this study, we are interested in characterizing the anticancer activity of the A.testudineus antimicrobial peptides (AMPs). The mucus was extracted, fractioned, and subjected to antibacterial activity testing to confirm the fish's AMPs production. The cytotoxic activity of each fraction was also identified. Fraction 2 (F2), which shows toxicity against MCF7 and MDA-MB-231 were sent for peptide sequencing to identify the bioactive peptide. The two peptides were then synthetically produced and subjected to cytotoxic assay to prove their efficacy against cancer cell lines. The IC50 for AtMP1 against MCF7 and MDA-MB-231 were 8.25 ± 0.14 μg/ml and 9.35 ± 0.25 μg/ml respectively, while for AtMP2 it is 5.89 ± 0.14 μg/ml and 6.97 ± 0.24 μg/ml respectively. AtMP1 and AtMP2 treatment for 48 h induced breast cancer cell cycle arrest and apoptosis by upregulating the p53, which lead to upregulate pro-apoptotic BAX gene and downregulate the anti-apoptotic BCL-2 gene, consequently, trigger the activation of the caspase-3. This interaction was supported by docking analysis (QuickDBD, HPEPDOCK, and ZDOCK) and immunoprecipitation. This study provided new prospects in the development of highly effective and selective cancer therapeutics based on antimicrobial peptides.
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Affiliation(s)
- Ahmed Abdul Kareem Najm
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Ahmad Azfaralariff
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia.,Innovative Center for Confectionery Technology (MANIS), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Herryawan Ryadi Eziwar Dyari
- Department of Earth Sciences and Environmental, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Babul Airianah Othman
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Muhammad Shahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Nahid Khalili
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia
| | - Douglas Law
- Faculty of Health and Life Sciences, Inti International University, Persiaran Perdana BBN Putra Nilai, 71800, Nilai, Negeri Sembilan, Malaysia
| | - Sharifah Sakinah Syed Alwi
- Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Shazrul Fazry
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia. .,Innovative Center for Confectionery Technology (MANIS), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia. .,Chini Lake Research Centre, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor Darul Ehsan, Malaysia.
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14
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Xiong Z, Lo HP, McMahon KA, Parton RG, Hall TE. Proximity Dependent Biotin Labelling in Zebrafish for Proteome and Interactome Profiling. Bio Protoc 2021; 11:e4178. [PMID: 34722825 DOI: 10.21769/bioprotoc.4178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/02/2022] Open
Abstract
Identification of protein interaction networks is key for understanding intricate biological processes, but mapping such networks is challenging with conventional biochemical methods, especially for weak or transient interactions. Proximity-dependent biotin labelling (BioID) using promiscuous biotin ligases and mass spectrometry (MS)-based proteomics has emerged in the past decade as a powerful method for probing local proteomes and protein interactors. Here, we describe the application of an engineered biotin ligase, TurboID, for proteomic mapping and interactor screening in vivo in zebrafish. We generated novel transgenic zebrafish lines that express TurboID fused to a conditionally stabilised GFP-binding nanobody, dGBP, which targets TurboID to the GFP-tagged proteins of interest. The TurboID-dGBP zebrafish lines enable proximity-dependent biotin labelling in live zebrafish simply through outcrossing with existing GFP-tagged lines. Here, we outline a detailed protocol of the BLITZ method (Biotin Labelling In Tagged Zebrafish) for utilising TurboID-dGBP fish lines to map local proteomes and screen novel interactors. Graphic abstract: Schematic overview of the BLITZ method. TurboID-dGBP fish are crossed with GFP-tagged lines to obtain embryos co-expressing TurboID-dGBP (indicated by mKate2) and the GFP-POI (protein of interest). Embryos expressing only TurboID are used as a negative control. Embryos (2 to 7 dpf) are incubated overnight with a 500 μM biotin-supplemented embryo medium. This biotin incubation step allows TurboID to catalyse proximity-dependent biotinylation in live zebrafish embryos. After biotin incubation, embryos are solubilised in lysis buffer, and free biotin is removed using a PD-10 desalting column. The biotinylated proteins are captured by streptavidin affinity purification, and captured proteins are analysed by MS sequencing.
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Affiliation(s)
- Zherui Xiong
- Institute for Molecular Bioscience, the University of Queensland, Queensland 4072, Australia
| | - Harriet P Lo
- Institute for Molecular Bioscience, the University of Queensland, Queensland 4072, Australia
| | - Kerrie-Ann McMahon
- Institute for Molecular Bioscience, the University of Queensland, Queensland 4072, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, the University of Queensland, Queensland 4072, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas E Hall
- Institute for Molecular Bioscience, the University of Queensland, Queensland 4072, Australia
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15
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Li H, Frankenfield AM, Houston R, Sekine S, Hao L. Thiol-Cleavable Biotin for Chemical and Enzymatic Biotinylation and Its Application to Mitochondrial TurboID Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2358-2365. [PMID: 33909971 PMCID: PMC8898397 DOI: 10.1021/jasms.1c00079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein biotinylation via chemical or enzymatic reactions is often coupled with streptavidin-based enrichment and on-bead digestion in numerous biological applications. However, the popular on-bead digestion method faces major challenges of streptavidin contamination, overwhelming signals from endogenous biotinylated proteins, the lost information on biotinylation sites, and limited sequence coverage of enriched proteins. Here, we explored thiol-cleavable biotin as an alternative approach to elute biotinylated proteins from streptavidin-coated beads for both chemical biotinylation and biotin ligase-based proximity labeling. All possible amino acid sites for biotinylation were thoroughly evaluated in addition to the primary lysine residue. We found that biotinylation at lysine residues notably reduces the trypsin digestion efficiency, which can be mitigated by the thiol-cleavable biotinylation method. We then evaluated the applicability of thiol-cleavable biotin as a substrate for proximity labeling in living cells, where TurboID biotin ligase was engineered onto the mitochondrial inner membrane facing the mitochondrial matrix. As a proof-of-principle study, thiol-cleavable biotin-assisted TurboID proteomics achieved remarkable intraorganelle spatial resolution with significantly enriched proteins localized in the mitochondrial inner membrane and mitochondrial matrix.
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Affiliation(s)
- Haorong Li
- Department of Chemistry, The George Washington University, Science and Engineering Hall, 800 22nd Street, NW, Washington, DC 20052, United States
| | - Ashley M Frankenfield
- Department of Chemistry, The George Washington University, Science and Engineering Hall, 800 22nd Street, NW, Washington, DC 20052, United States
| | - Ryan Houston
- Aging Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh, Bridgeside Point I, 100 Technology Drive, Pittsburgh, Pennsylvania 15219, United States
| | - Shiori Sekine
- Aging Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh, Bridgeside Point I, 100 Technology Drive, Pittsburgh, Pennsylvania 15219, United States
| | - Ling Hao
- Department of Chemistry, The George Washington University, Science and Engineering Hall, 800 22nd Street, NW, Washington, DC 20052, United States
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16
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Garcia BCB, Horie M, Kojima S, Makino A, Tomonaga K. BUD23-TRMT112 interacts with the L protein of Borna disease virus and mediates the chromosomal tethering of viral ribonucleoproteins. Microbiol Immunol 2021; 65:492-504. [PMID: 34324219 DOI: 10.1111/1348-0421.12934] [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: 05/27/2021] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 11/28/2022]
Abstract
Persistent intranuclear infection is an uncommon infection strategy among RNA viruses. However, Borna disease virus 1 (BoDV-1), a nonsegmented, negative-strand RNA virus, maintains viral infection in the cell nucleus by forming structured aggregates of viral ribonucleoproteins (vRNPs), and by tethering these vRNPs onto the host chromosomes. To better understand the nuclear infection strategy of BoDV-1, we determined the host protein interactors of the BoDV-1 large (L) protein. By proximity-dependent biotinylation, we identified several nuclear host proteins interacting with BoDV-1 L, one of which is TRMT112, a partner of several RNA methyltransferases (MTase). TRMT112 binds with BoDV-1 L at the RNA-dependent RNA polymerase domain, together with BUD23, an 18S rRNA MTase and 40S ribosomal maturation factor. We then discovered that BUD23-TRMT112 mediates the chromosomal tethering of BoDV-1 vRNPs, and that the MTase activity is necessary in the tethering process. These findings provide us a better understanding on how nuclear host proteins assist the chromosomal tethering of BoDV-1, as well as new prospects of host-viral interactions for intranuclear infection strategy of orthobornaviruses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bea Clarise B Garcia
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto
| | - Masayuki Horie
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto.,Hakubi Center for Advanced Research, Kyoto University, Kyoto
| | - Shohei Kojima
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto
| | - Akiko Makino
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Institute for Frontier Life and Medical Sciences (inFRONT), Kyoto University, Kyoto.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto.,Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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17
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Cheah JS, Jacobs KA, Lai TW, Caballelo R, Yee JL, Ueda S, Heinrich V, Yamada S. Spatial proximity of proteins surrounding zyxin under force-bearing conditions. Mol Biol Cell 2021; 32:1221-1228. [PMID: 33909446 PMCID: PMC8351546 DOI: 10.1091/mbc.e19-10-0568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Sensing physical forces is a critical first step in mechano-transduction of cells. Zyxin, a LIM domain-containing protein, is recruited to force-bearing actin filaments and is thought to repair and strengthen them. Yet, the precise force-induced protein interactions surrounding zyxin remain unclear. Using BioID analysis, we identified proximal proteins surrounding zyxin under normal and force-bearing conditions by label-free mass spectrometry analysis. Under force-bearing conditions, increased biotinylation of α-actinin 1, α-actinin 4, and AFAP1 were detected, and these proteins accumulated along force-bearing actin fibers independently from zyxin, albeit at a lower intensity than zyxin. VASP also accumulated along force-bearing actin fibers in a zyxin-dependent manner, but the biotinylation of VASP remained constant regardless of force, supporting the model of a free zyxin-VASP complex in the cytoplasm being corecruited to tensed actin fibers. In addition, ARHGAP42, a RhoA GAP, was also identified as a proximal protein of zyxin and colocalized with zyxin along contractile actin bundles. The overexpression of ARHGAP42 reduced the rate of small wound closure, a zyxin-dependent process. These results demonstrate that the application of proximal biotinylation can resolve the proximity and composition of protein complexes as a function of force, which had not been possible with traditional biochemical analysis.
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Affiliation(s)
- Joleen S Cheah
- Biomedical Engineering Department, University of California Davis, Davis, CA 95616.,Biosciences Program, Stanford University, Stanford, CA 94305
| | - Kyle A Jacobs
- Biomedical Engineering Department, University of California Davis, Davis, CA 95616
| | - Tzu Wei Lai
- Biomedical Engineering Department, University of California Davis, Davis, CA 95616
| | - Reca Caballelo
- Biomedical Engineering Department, University of California Davis, Davis, CA 95616
| | - Jacqueline L Yee
- Biomedical Engineering Department, University of California Davis, Davis, CA 95616
| | - Shuji Ueda
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan 657
| | - Volkmar Heinrich
- Biomedical Engineering Department, University of California Davis, Davis, CA 95616
| | - Soichiro Yamada
- Biomedical Engineering Department, University of California Davis, Davis, CA 95616
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18
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Capon PK, Horsfall AJ, Li J, Schartner EP, Khalid A, Purdey MS, McLaughlin RA, Abell AD. Protein detection enabled using functionalised silk-binding peptides on a silk-coated optical fibre. RSC Adv 2021; 11:22334-22342. [PMID: 35480827 PMCID: PMC9034238 DOI: 10.1039/d1ra03584c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/04/2021] [Indexed: 11/21/2022] Open
Abstract
We report a new approach to functionalise optical fibres to enable protein sensing, which controls the sensor molecule location either within the fibre tip coating or isolated to its exterior. This control dictates suitability for protein sensing.
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Affiliation(s)
- Patrick K. Capon
- School of Physical Sciences
- The University of Adelaide
- Adelaide
- Australia
- Institute for Photonics and Advanced Sensing
| | - Aimee J. Horsfall
- School of Physical Sciences
- The University of Adelaide
- Adelaide
- Australia
- Institute for Photonics and Advanced Sensing
| | - Jiawen Li
- Institute for Photonics and Advanced Sensing
- The University of Adelaide
- Adelaide
- Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics
| | - Erik P. Schartner
- School of Physical Sciences
- The University of Adelaide
- Adelaide
- Australia
- Institute for Photonics and Advanced Sensing
| | - Asma Khalid
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics
- Australia
- Department of Physics
- School of Science
- RMIT University
| | - Malcolm S. Purdey
- School of Physical Sciences
- The University of Adelaide
- Adelaide
- Australia
- Institute for Photonics and Advanced Sensing
| | - Robert A. McLaughlin
- Institute for Photonics and Advanced Sensing
- The University of Adelaide
- Adelaide
- Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics
| | - Andrew D. Abell
- School of Physical Sciences
- The University of Adelaide
- Adelaide
- Australia
- Institute for Photonics and Advanced Sensing
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19
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Shafraz O, Xie B, Yamada S, Sivasankar S. Mapping transmembrane binding partners for E-cadherin ectodomains. Proc Natl Acad Sci U S A 2020; 117:31157-31165. [PMID: 33229577 PMCID: PMC7733791 DOI: 10.1073/pnas.2010209117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We combine proximity labeling and single molecule binding assays to discover transmembrane protein interactions in cells. We first screen for candidate binding partners by tagging the extracellular and cytoplasmic regions of a "bait" protein with BioID biotin ligase and identify proximal proteins that are biotin tagged on both their extracellular and intracellular regions. We then test direct binding interactions between proximal proteins and the bait, using single molecule atomic force microscope binding assays. Using this approach, we identify binding partners for the extracellular region of E-cadherin, an essential cell-cell adhesion protein. We show that the desmosomal proteins desmoglein-2 and desmocollin-3, the focal adhesion protein integrin-α2β1, the receptor tyrosine kinase ligand ephrin-B1, and the classical cadherin P-cadherin, all directly interact with E-cadherin ectodomains. Our data shows that combining extracellular and cytoplasmic proximal tagging with a biophysical binding assay increases the precision with which transmembrane ectodomain interactors can be identified.
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Affiliation(s)
- Omer Shafraz
- Department of Biomedical Engineering, University of California, Davis, CA 95616
| | - Bin Xie
- Biophysics Graduate Group, University of California, Davis, CA 95616
| | - Soichiro Yamada
- Department of Biomedical Engineering, University of California, Davis, CA 95616
| | - Sanjeevi Sivasankar
- Department of Biomedical Engineering, University of California, Davis, CA 95616;
- Biophysics Graduate Group, University of California, Davis, CA 95616
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20
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Frankenfield AM, Fernandopulle MS, Hasan S, Ward ME, Hao L. Development and Comparative Evaluation of Endolysosomal Proximity Labeling-Based Proteomic Methods in Human iPSC-Derived Neurons. Anal Chem 2020; 92:15437-15444. [DOI: 10.1021/acs.analchem.0c03107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ashley M. Frankenfield
- Department of Chemistry, The George Washington University, Science and Engineering Hall, Suite 4000, 800 22nd Street, NW, Washington, District of Columbia 20052, United States
| | - Michael S. Fernandopulle
- National Institute of Neurological Disorders and Stroke, NIH, Building 35-2A, 35 Convent Drive, Bethesda, Maryland 20892, United States
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Hills Road, CB2 0XY, UK
| | - Saadia Hasan
- National Institute of Neurological Disorders and Stroke, NIH, Building 35-2A, 35 Convent Drive, Bethesda, Maryland 20892, United States
| | - Michael E. Ward
- National Institute of Neurological Disorders and Stroke, NIH, Building 35-2A, 35 Convent Drive, Bethesda, Maryland 20892, United States
| | - Ling Hao
- Department of Chemistry, The George Washington University, Science and Engineering Hall, Suite 4000, 800 22nd Street, NW, Washington, District of Columbia 20052, United States
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21
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St-Germain JR, Samavarchi Tehrani P, Wong C, Larsen B, Gingras AC, Raught B. Variability in Streptavidin-Sepharose Matrix Quality Can Significantly Affect Proximity-Dependent Biotinylation (BioID) Data. J Proteome Res 2020; 19:3554-3561. [PMID: 32628020 DOI: 10.1021/acs.jproteome.0c00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to their ease of use and high binding affinity, streptavidin-based purification tools have become widely used for isolating biotinylated compounds from complex mixtures. We and others routinely use streptavidin-sepharose matrices to isolate biotinylated polypeptides generated in proximity-dependent biotinylation approaches, such as BioID or APEX. However, we noted sporadic, substantial variation in the quality of BioID experiments performed in the same laboratories over time, using seemingly identical protocols. Identifying the source of this problem, here, we highlight considerable variability in streptavidin contamination derived from different production lots of streptavidin-sepharose beads from the same manufacturer and demonstrate that high levels of streptavidin peptide contamination can have detrimental effects on BioID data. We also describe two simple, rapid approaches to assess the degree of streptavidin "shedding" from individual lots of the sepharose matrix before use to avoid the use of lower quality reagent.
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Affiliation(s)
- Jonathan R St-Germain
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Payman Samavarchi Tehrani
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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22
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Mendes A, Jühlen R, Bousbata S, Fahrenkrog B. Disclosing the Interactome of Leukemogenic NUP98-HOXA9 and SET-NUP214 Fusion Proteins Using a Proteomic Approach. Cells 2020; 9:E1666. [PMID: 32664447 PMCID: PMC7407662 DOI: 10.3390/cells9071666] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
The interaction of oncogenes with cellular proteins is a major determinant of cellular transformation. The NUP98-HOXA9 and SET-NUP214 chimeras result from recurrent chromosomal translocations in acute leukemia. Functionally, the two fusion proteins inhibit nuclear export and interact with epigenetic regulators. The full interactome of NUP98-HOXA9 and SET-NUP214 is currently unknown. We used proximity-dependent biotin identification (BioID) to study the landscape of the NUP98-HOXA9 and SET-NUP214 environments. Our results suggest that both fusion proteins interact with major regulators of RNA processing, with translation-associated proteins, and that both chimeras perturb the transcriptional program of the tumor suppressor p53. Other cellular processes appear to be distinctively affected by the particular fusion protein. NUP98-HOXA9 likely perturbs Wnt, MAPK, and estrogen receptor (ER) signaling pathways, as well as the cytoskeleton, the latter likely due to its interaction with the nuclear export receptor CRM1. Conversely, mitochondrial proteins and metabolic regulators are significantly overrepresented in the SET-NUP214 proximal interactome. Our study provides new clues on the mechanistic actions of nucleoporin fusion proteins and might be of particular relevance in the search for new druggable targets for the treatment of nucleoporin-related leukemia.
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Affiliation(s)
- Adélia Mendes
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium; (R.J.); (S.B.)
| | - Ramona Jühlen
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium; (R.J.); (S.B.)
- Present address: Institute of Biochemistry and Molecular Cell Biology, RWTH Aachen University, 52074 Aachen, Germany
| | - Sabrina Bousbata
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium; (R.J.); (S.B.)
| | - Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium; (R.J.); (S.B.)
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23
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Pomplun S, Shugrue CR, Schmitt AM, Schissel CK, Farquhar CE, Pentelute BL. Secondary Amino Alcohols: Traceless Cleavable Linkers for Use in Affinity Capture and Release. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sebastian Pomplun
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Christopher R. Shugrue
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | | | - Carly K. Schissel
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Charlotte E. Farquhar
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
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24
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Boussardon C, Przybyla-Toscano J, Carrie C, Keech O. Tissue-specific isolation of Arabidopsis/plant mitochondria - IMTACT (isolation of mitochondria tagged in specific cell types). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:459-473. [PMID: 32057155 DOI: 10.1111/tpj.14723] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/07/2020] [Accepted: 02/04/2020] [Indexed: 05/19/2023]
Abstract
Plant cells contain numerous subcompartments with clearly delineated metabolic functions. Mitochondria represent a very small fraction of the total cell volume and yet are the site of respiration and thus crucial for cells throughout all developmental stages of a plant's life. As such, their isolation from the rest of the cellular components is a basic requirement for numerous biochemical and physiological experiments. Although procedures exist to isolate plant mitochondria from different organs (i.e. leaves, roots, tubers, etc.), they are often tedious and do not provide resolution at the tissue level (i.e. phloem, mesophyll or pollen). Here, we present a novel method called IMTACT (isolation of mitochondria tagged in specific cell types), developed in Arabidopsis thaliana (Arabidopsis) that involves biotinylation of mitochondria in a tissue-specific manner using transgenic lines expressing a synthetic version of the OM64 (Outer Membrane 64) gene combined with BLRP and the BirA biotin ligase gene. Tissue specificity is achieved with cell-specific promoters (e.g. CAB3 and SUC2). Labeled mitochondria from crude extracts are retained by magnetic beads, allowing the simple and rapid isolation of highly pure and intact organelles from organs or specific tissues. For example, we could show that the mitochondrial population from mesophyll cells was significantly larger in size than the mitochondrial population isolated from leaf companion cells. To facilitate the applicability of this method in both wild-type and mutant Arabidopsis plants we generated a set of OM64-BLRP one-shot constructs with different selection markers and tissue-specific promoters.
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Affiliation(s)
- Clément Boussardon
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
| | | | - Chris Carrie
- Department Biologie I - Botanik, Ludwig-Maximilians-Universität München, Großhadernerstrasse 2-4, Planegg-Martinsried, 82152, Germany
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90187, Umeå, Sweden
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25
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Hahn F, Niesar A, Wangen C, Wild M, Grau B, Herrmann L, Capci A, Adrait A, Couté Y, Tsogoeva SB, Marschall M. Target verification of artesunate-related antiviral drugs: Assessing the role of mitochondrial and regulatory proteins by click chemistry and fluorescence labeling. Antiviral Res 2020; 180:104861. [PMID: 32590041 DOI: 10.1016/j.antiviral.2020.104861] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 12/22/2022]
Abstract
Human cytomegalovirus (HCMV) infection is associated with serious pathology such as transplant rejection or embryonic developmental defects. Antiviral treatment with currently available drugs targeting viral enzymes is often accompanied with severe side effects and the occurrence of drug-resistant viruses. For this reason, novel ways of anti-HCMV therapy focusing on so far unexploited small molecules, targets and mechanisms are intensively studied. Recently, we described the pronounced antiviral activity of the artesunate-related class of trioxane compounds, comprising NF-κB/signaling inhibitors like the trimeric derivative TF27, which proved to be highly active in a nanomolar range both in vitro and in vivo. Here, we extend this analysis by presenting further TF27/artesunate-derived antiviral compounds designed for their specific use in target verification by click chemistry applied in fluorescence labeling and tag affinity strategies. Our main findings are as follows: (i) compounds TF27, BG95, AC98 and AC173 exert strong inhibitory activity against HCMV replication in cultured primary human cells, (ii) autofluorescence activity could be quantitatively detected for BG95 and AC98, and confocal fluorescence imaging revealed accumulation in mitochondria, (iii) postulated cellular targets including mitochondrial proteins were down-regulated upon TF27 treatment, (iv) a click chemistry-based protocol of target enrichment was established, and (v) mass spectrometry-based proteomic analysis, using proteins from HCMV-infected fibroblasts covalently interacting with AC173, revealed a refined list of targets. Combined, data strongly suggest a complex mode of antiviral drug-target interaction of artesunate-related compounds, now highlighting potential roles of mitochondrial, NF-κB pathway proteins, exportins and possibly more. This strategy may further promote antiviral drug development on the basis of pharmacologically optimized trioxane derivatives.
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Affiliation(s)
- Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Aischa Niesar
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Markus Wild
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
| | - Benedikt Grau
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany.
| | - Lars Herrmann
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany.
| | - Aysun Capci
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany.
| | - Annie Adrait
- Univ. Grenoble Alpes, CEA, Inserm, IRIG, BGE, 38000, Grenoble, France.
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, Inserm, IRIG, BGE, 38000, Grenoble, France.
| | - Svetlana B Tsogoeva
- Organic Chemistry Chair I and Interdisciplinary Center for Molecular Materials (ICMM), Friedrich-Alexander University of Erlangen-Nürnberg, Nikolaus Fiebiger-Straße 10, 91058, Erlangen, Germany.
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany.
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26
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Sun N, Wang Y, Wang J, Sun W, Yang J, Liu N. Highly Efficient Peptide-Based Click Chemistry for Proteomic Profiling of Nascent Proteins. Anal Chem 2020; 92:8292-8297. [PMID: 32434323 DOI: 10.1021/acs.analchem.0c00594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ningning Sun
- Central Laboratory, The Second Hospital of Jilin University, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Yong Wang
- College of Life Science, Shenzhen University, Shenzhen, China
| | - Jun Wang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Wanchun Sun
- Central Laboratory, The Second Hospital of Jilin University, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Jingbo Yang
- Central Laboratory, The Second Hospital of Jilin University, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Ning Liu
- Central Laboratory, The Second Hospital of Jilin University, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
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27
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Pomplun S, Shugrue CR, Schmitt AM, Schissel CK, Farquhar CE, Pentelute BL. Secondary Amino Alcohols: Traceless Cleavable Linkers for Use in Affinity Capture and Release. Angew Chem Int Ed Engl 2020; 59:11566-11572. [PMID: 32227406 DOI: 10.1002/anie.202003478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/24/2020] [Indexed: 11/09/2022]
Abstract
Capture and release of peptides is often a critical operation in the pathway to discovering materials with novel functions. However, the best methods for efficient capture impede facile release. To overcome this challenge, we report linkers based on secondary amino alcohols for the release of peptides after capture. These amino alcohols are based on serine (seramox) or isoserine (isoseramox) and can be incorporated into peptides during solid-phase peptide synthesis through reductive amination. Both linkers are quantitatively cleaved within minutes under NaIO4 treatment. Cleavage of isoseramox produced a native peptide N-terminus. This linker also showed broad substrate compatibility; incorporation into a synthetic peptide library resulted in the identification of all sequences by nanoLC-MS/MS. The linkers are cell compatible; a cell-penetrating peptide that contained this linker was efficiently captured and identified after uptake into cells. These findings suggest that such secondary amino alcohol based linkers might be suitable tools for peptide-discovery platforms.
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Affiliation(s)
- Sebastian Pomplun
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Christopher R Shugrue
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Adeline M Schmitt
- Université de Strasbourg, 4 rue Blaise Pascal, 67000, Strasbourg, France
| | - Carly K Schissel
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Charlotte E Farquhar
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Bradley L Pentelute
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
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28
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A simple method for non-denaturing purification of biotin-tagged proteins through competitive elution with free biotin. Biotechniques 2019; 68:41-44. [PMID: 31825236 DOI: 10.2144/btn-2019-0088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The use of avidin or streptavidin in the purification of biotinylated proteins has been highly restricted due to the harsh and denaturing elution conditions. Here, we use biotinylated bovine serum albumin as a working model to demonstrate a simple and rapid method for biotin-tagged protein purification under non-denaturing conditions. The biotinylated bovine serum albumin is specifically bound to the anti-biotin antibody agarose beads and competitively eluted with free biotin under near-neutral conditions. The optimized elution conditions include using 4 mg/ml biotin (pH 8.5) as the elution buffer and allowing the buffer to incubate with agarose beads for 30 min prior to elution. The elution recovery rate is over 85% without apparent protein denaturation. The method is applicable for both immunoprecipitation and column chromatography.
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29
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Gopinathan P, Sinha A, Chung YD, Shiesh SC, Lee GB. Optimization of an enzyme linked DNA aptamer assay for cardiac troponin I detection: synchronous multiple sample analysis on an integrated microfluidic platform. Analyst 2019; 144:4943-4951. [PMID: 31317135 DOI: 10.1039/c9an00779b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this study, an enzyme linked DNA aptamer based assay was optimized for human cardiac troponin I (cTnI) detection which is a prominent biomarker for acute myocardial infarction (AMI), on an integrated microfluidic platform. This platform allowed for the multiplex detection of six samples (5 μL per sample), and only 30 min were required for detection. First, cTnI-specific aptamers were surface-coated on magnetic beads. Bead-captured proteins were allowed to bind to a primary cTnI antibody and then to a secondary antibody labelled with horseradish peroxidase. Finally, chemiluminescence intensities were detected for quantification of cTnI. Purified proteins, serum from AMI patients and unknown serum samples were used to test the efficacy of the on-chip system. The limit of detection was measured to be only 12 ng L-1, and off-target effects from other proteins were minimal. This sensitive, cTnI-specific aptamer-based assay could consequently be used for reliable diagnosis of AMI.
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Affiliation(s)
- Priya Gopinathan
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
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30
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Barshop WD, Kim HJ, Fan X, Sha J, Rayatpisheh S, Wohlschlegel JA. Chemical Derivatization of Affinity Matrices Provides Protection from Tryptic Proteolysis. J Proteome Res 2019; 18:3586-3596. [PMID: 31498634 DOI: 10.1021/acs.jproteome.9b00254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enrichment of biotinylated proteins using immobilized streptavidin has become a staple methodology for affinity purification-based proteomics. Many of these workflows rely upon tryptic digestion to elute streptavidin-captured moieties from the beads. The concurrent release of high amounts of streptavidin-derived peptides into the digested sample, however, can significantly hamper the effectiveness of downstream proteomic analyses by increasing the complexity and dynamic range of the mixture. Here, we describe a strategy for the chemical derivatization of streptavidin that renders it largely resistant to proteolysis by trypsin and thereby dramatically reduces the amount of streptavidin contamination in the sample. This rapid and robust approach improves the effectiveness of mass spectrometry-based characterization of streptavidin-purified samples making it broadly useful for a wide variety of applications. In addition, we show that this chemical protection strategy can also be applied to other affinity matrices including immobilized antibodies against HA epitopes.
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Affiliation(s)
- William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - Hee Jong Kim
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - Xiaorui Fan
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - Jihui Sha
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - Shima Rayatpisheh
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine , University of California-Los Angeles , Los Angeles , California 951737 , United States
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31
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Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC. Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID. eLife 2019; 8:e47864. [PMID: 31535972 PMCID: PMC6791687 DOI: 10.7554/elife.47864] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/15/2019] [Indexed: 12/15/2022] Open
Abstract
Defining specific protein interactions and spatially or temporally restricted local proteomes improves our understanding of all cellular processes, but obtaining such data is challenging, especially for rare proteins, cell types, or events. Proximity labeling enables discovery of protein neighborhoods defining functional complexes and/or organellar protein compositions. Recent technological improvements, namely two highly active biotin ligase variants (TurboID and miniTurbo), allowed us to address two challenging questions in plants: (1) what are in vivo partners of a low abundant key developmental transcription factor and (2) what is the nuclear proteome of a rare cell type? Proteins identified with FAMA-TurboID include known interactors of this stomatal transcription factor and novel proteins that could facilitate its activator and repressor functions. Directing TurboID to stomatal nuclei enabled purification of cell type- and subcellular compartment-specific proteins. Broad tests of TurboID and miniTurbo in Arabidopsis and Nicotiana benthamiana and versatile vectors enable customization by plant researchers.
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Affiliation(s)
- Andrea Mair
- Department of BiologyStanford UniversityStanfordUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Shou-Ling Xu
- Department of Plant BiologyCarnegie Institution for ScienceStanfordUnited States
| | - Tess C Branon
- Department of BiologyStanford UniversityStanfordUnited States
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeUnited States
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of ChemistryStanford UniversityStanfordUnited States
| | - Alice Y Ting
- Department of BiologyStanford UniversityStanfordUnited States
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of ChemistryStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Dominique C Bergmann
- Department of BiologyStanford UniversityStanfordUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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32
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Jinn WS, Shin MK, Kang B, Oh S, Moon CE, Mun B, Ji YW, Lee HK, Haam S. A visually distinguishable light interfering bioresponsive silica nanoparticle hydrogel sensor fabricated through the molecular imprinting technique. J Mater Chem B 2019; 7:7120-7128. [DOI: 10.1039/c9tb01579e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methods of the early detection of diseases are based on recognition of the smallest change in the levels of a disease-specific biomarker in body fluids.
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Affiliation(s)
- Woo Seok Jinn
- Department of Chemical and Biomolecular Engineering
- College of Engineering
- Yonsei University
- Seoul 120-749
- Republic of Korea
| | - Moo-Kwang Shin
- Department of Chemical and Biomolecular Engineering
- College of Engineering
- Yonsei University
- Seoul 120-749
- Republic of Korea
| | - Byunghoon Kang
- BioNanotechnology Research Center
- Korea Research Institue of Bioscience and Biotechnology(KRIBB)
- Daejeon 34141
- Republic of Korea
| | - Seungjae Oh
- Department of Radiology
- College of Medicine
- Yonsei University
- Seoul 120-752
- Republic of Korea
| | - Chae-Eun Moon
- Department of Ophthalmology
- College of Medicine
- Yonsei University
- Seoul 120-752
- Republic of Korea
| | - Byeonggeol Mun
- Department of Chemical and Biomolecular Engineering
- College of Engineering
- Yonsei University
- Seoul 120-749
- Republic of Korea
| | - Yong Woo Ji
- Department of Ophthalmology
- National Health Insurance Service Ilsan Hospital
- Goyang 10444
- Republic of Korea
| | - Hyung Keun Lee
- Department of Ophthalmology
- College of Medicine
- Yonsei University
- Seoul 120-752
- Republic of Korea
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering
- College of Engineering
- Yonsei University
- Seoul 120-749
- Republic of Korea
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33
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Liu G, Cao C, Ni S, Feng S, Wei H. On-chip structure-switching aptamer-modified magnetic nanobeads for the continuous monitoring of interferon-gamma ex vivo. MICROSYSTEMS & NANOENGINEERING 2019; 5:35. [PMID: 31636925 PMCID: PMC6799845 DOI: 10.1038/s41378-019-0074-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/18/2019] [Accepted: 05/27/2019] [Indexed: 05/04/2023]
Abstract
Cytokines are cell signaling molecules that indicate the health status of the body. In this study, we developed a microfluidic device integrated with structure-switching aptamers capable of continuously tracking the concentration of the cytokine interferon gamma (IFN-γ) in cell culture medium and blood serum. First, a ferrocene (Fc)-labeled structure-switching signaling aptamer with a hairpin structure targeting IFN-γ was immobilized on magnetic nanobeads by the strongest noncovalent interactions between streptavidin and biotin. The aptamer-modified magnetic nanobeads were trapped on a customized microfluidic chip by a magnetic field to form the sensing interface. The binding of IFN-γ could trigger the hairpin structure of the aptamer to unfold, pushing Fc redox molecules away from the sensing interface and consequently switching off the electrochemical signal. The change in the redox current of Fc was quantitatively related to the concentration of IFN-γ in a linear range of 10-500 pg mL-1 and with the lowest detection limit of 6 pg mL-1. This microfluidic device was specific to IFN-γ in the presence of overabundant serum proteins and allowed the continuous monitoring of IFN-γ without adding exogenous reagents. It provided a universal point-of-care biosensing platform for the real-time detection of a spectrum of analytes.
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Affiliation(s)
- Guozhen Liu
- Graduate School of Biomedical Engineering, ARC Centre of Excellence in Nanoscale Biophotonics (CNBP), Faculty of Engineering, The University of New South Wales, Sydney, NSW 2052 Australia
- Australian Centre for NanoMedicine, UNSW Sydney, Sydney, NSW 2052 Australia
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, 430079 Wuhan, PR China
| | - Chaomin Cao
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, 430079 Wuhan, PR China
| | - Shengnan Ni
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, 430079 Wuhan, PR China
| | - Shilun Feng
- School of Engineering, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109 Australia
| | - Hui Wei
- International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, 430079 Wuhan, PR China
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