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Han G, Su Y, Mao Q, Han Z, Sun J. Identification and functional characterization of annexin A2 in half-smooth tongue sole (Cynoglossus semilaevis). Fish & Shellfish Immunology 2024; 148:109492. [PMID: 38467321 DOI: 10.1016/j.fsi.2024.109492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
Annexin A2 (AnxA2), belonging to the annexin family, plays a crucial role in immune responses. In this study, the cDNA of the AnxA2 gene was identified in half-smooth tongue sole, Cynoglossus semilaevis. The transcript of AnxA2 gene in C. semilaevis (CsAnxA2) showed broad tissue distribution, with the highest expression level observed in the gut. CsAnxA2 expression was significantly up-regulated in the intestine, spleen, and kidney tissues following exposure to Shewanella algae. Immunohistochemical staining revealed that CsAnxA2 was predominantly expressed in epithelial cells and significantly elevated after S. algae challenge. Subcellular localization showed that CsAnxA2 was primarily localized in the cytoplasmic compartment. Moreover, proinflammatory cytokines (IL-6, IL-8 and IL-1β) exhibited significant upregulation after CsAnxA2 was overexpressed in vivo. One hundred and fifty-eight CsAnxA2-interacting proteins were captured in the intestinal tissue, showing the top two normalized abundance observed for actin beta (ACTB) and protein S100-A10 (p11). Fifty-four high abundance CsAnxA2-interacting proteins (HIPs) were primary enriched in ten pathways, with the top three significantly enriched pathways being Salmonella infection, glycolysis/gluconeogenesis, and peroxisome proliferator-activated receptor (PPAR) signaling pathway. These results provide valuable information for further investigation into the functional mechanism of AnxA2 in C. semilaevis.
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Affiliation(s)
- Guowei Han
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province), Tianjin Agricultural University, Tianjin, 300384, China; Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Yufeng Su
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Qing Mao
- Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Zhuoran Han
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province), Tianjin Agricultural University, Tianjin, 300384, China; Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
| | - Jingfeng Sun
- Key Laboratory of Smart Breeding (Co-construction by Ministry and Province), Tianjin Agricultural University, Tianjin, 300384, China; Tianjin Key Lab of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China.
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2
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Wang W, Xu L, Jiang G, Li Z, Bi YH, Zhou ZG. Characterization of a novel γ-type carbonic anhydrase, Sjγ-CA2, in Saccharina japonica: Insights into carbon concentration mechanism in macroalgae. Int J Biol Macromol 2024; 263:130506. [PMID: 38423426 DOI: 10.1016/j.ijbiomac.2024.130506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Carbonic anhydrase (CA) is a crucial component of CO2-concentrating mechanism (CCM) in macroalgae. In Saccharina japonica, an important brown seaweed, 11 CAs, including 5 α-, 3 β-, and 3 γ-CAs, have been documented. Among them, one α-CA and one β-CA were localized in the periplasmic space, one α-CA was found in the chloroplast, and one γ-CA was situated in mitochondria. Notably, the known γ-CAs have predominantly been identified in mitochondria. In this study, we identified a chloroplastic γ-type CA, Sjγ-CA2, in S. japonica. Based on the reported amino acid sequence of Sjγ-CA2, the epitope peptide for monoclonal antibody production was selected as 165 Pro-305. After purification and specificity identification, anti-SjγCA2 monoclonal antibody was employed in immunogold electron microscopy. The results illustrated that Sjγ-CA2 was localized in the chloroplasts of both gametophytes and sporophytes of S. japonica. Subsequently, immunoprecipitation coupled with LC-MS/MS analysis revealed that Sjγ-CA2 mainly interacted with photosynthesis-related proteins. Moreover, the first 65 amino acids at N-terminal of Sjγ-CA2 was identified as the chloroplast transit peptide by the transient expression of GFP-SjγCA2 fused protein in tabacco. Real-time PCR results demonstrated an up-regulation of the transcription of Sjγ-CA2 gene in response to high CO2 concentration. These findings implied that Sjγ-CA2 might contribute to minimizing the leakage of CO2 from chloroplasts and help maintaining a high concentration of CO2 around Rubisco.
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Affiliation(s)
- Wen Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Ling Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Gang Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Zhi Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yan-Hui Bi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred By Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
| | - Zhi-Gang Zhou
- International Research Center for Marine Biosciences Conferred By Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
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3
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Jiang L, Li Y, Gu Y, Zheng J, Wei L, Wei M, Zou J, Wei C, Mo B, Pan L, Zhao L, Wang D. Identification of the Beta Subunit Fas1p of Fatty Acid Synthetase as an Interacting Partner of Yeast Calcium/Calmodulin-Dependent Protein Kinase Cmk2p Through Mass Spectrometry Analysis. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04891-w. [PMID: 38411936 DOI: 10.1007/s12010-024-04891-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
The calcium/calmodulin-dependent protein kinase II (CaMKII) is a mediator of calcium signals and regulates fatty acid metabolism in mammalian cells. Cmk2p is a yeast homolog of CaMKII and functions as a negative regulator of calcium signaling. However, its substrates remain to be identified. Combination of immunoprecipitation (IP) and mass spectrometry has been proven to be very useful for identification of interacting partner proteins and interactome. In this study, through these approaches, we have identified 65 and 110 potential Cmk2p-interacting proteins in yeast cells in the absence or presence of calcium stress, respectively. In yeast cells expressing both CMK2-HA and FAS1-GFP fusion proteins, in the absence or presence of calcium stress, less amounts of FAS1-GFP proteins are present in cell lysates after IP with anti-HA antibody than cell lysates before IP, while FAS1-GFP proteins are detected on both types of IP beads. However, as an internal control, similar amounts of Pgk1p proteins were detected in both after-IP and before-IP cell lysates but not on the IP beads. Therefore, our biochemical analysis demonstrates that the β subunit Fas1p of fatty acid synthetase interacts with Cmk2p in yeast cells independent of calcium stress. It is also interesting to note that, in addition to the expected 52-kDa CMK2-HA band, a faster-moving 48-kDa CMK2-HA band is present in the calcium-stressed cell lysate but not in the cell lysate without calcium stress. Our data would provide important clues for understanding the functions of CaMKII in the regulation of fatty acid metabolism as well as related diseases such as cancers, diabetes, and obesity.
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Affiliation(s)
- Linghuo Jiang
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China.
| | - Yiwu Li
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Yiying Gu
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
| | - Jiashi Zheng
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Liudan Wei
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, 530007, Guangxi, China
| | - Min Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Jie Zou
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Chunyu Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Bei Mo
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Lingxin Pan
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Lijiao Zhao
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
| | - Dan Wang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning, 530001, China
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Wang H, Ni X, Clark N, Randall K, Boeglin L, Chivukula S, Woo C, DeRosa F, Sun G. Absolute quantitation of human wild-type DNAI1 protein in lung tissue using a nanoLC-PRM-MS-based targeted proteomics approach coupled with immunoprecipitation. Clin Proteomics 2024; 21:8. [PMID: 38311768 PMCID: PMC10840268 DOI: 10.1186/s12014-024-09453-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/20/2024] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Dynein axonemal intermediate chain 1 protein (DNAI1) plays an essential role in cilia structure and function, while its mutations lead to primary ciliary dyskinesia (PCD). Accurate quantitation of DNAI1 in lung tissue is crucial for comprehensive understanding of its involvement in PCD, as well as for developing the potential PCD therapies. However, the current protein quantitation method is not sensitive enough to detect the endogenous level of DNAI1 in complex biological matrix such as lung tissue. METHODS In this study, a quantitative method combining immunoprecipitation with nanoLC-MS/MS was developed to measure the expression level of human wild-type (WT) DNAI1 protein in lung tissue. To our understanding, it is the first immunoprecipitation (IP)-MS based method for absolute quantitation of DNAI1 protein in lung tissue. The DNAI1 quantitation was achieved through constructing a standard curve with recombinant human WT DNAI1 protein spiked into lung tissue matrix. RESULTS This method was qualified with high sensitivity and accuracy. The lower limit of quantitation of human DNAI1 was 4 pg/mg tissue. This assay was successfully applied to determine the endogenous level of WT DNAI1 in human lung tissue. CONCLUSIONS The results clearly demonstrate that the developed assay can accurately quantitate low-abundance WT DNAI1 protein in human lung tissue with high sensitivity, indicating its high potential use in the drug development for DNAI1 mutation-caused PCD therapy.
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Affiliation(s)
- Hui Wang
- Translate Bio, a Sanofi Company, Lexington, MA, 02421, USA.
| | - Xiaoyan Ni
- Translate Bio, a Sanofi Company, Lexington, MA, 02421, USA
| | - Nicholas Clark
- Translate Bio, a Sanofi Company, Lexington, MA, 02421, USA
| | | | - Lianne Boeglin
- Translate Bio, a Sanofi Company, Lexington, MA, 02421, USA
| | | | - Caroline Woo
- Translate Bio, a Sanofi Company, Lexington, MA, 02421, USA
| | - Frank DeRosa
- Translate Bio, a Sanofi Company, Lexington, MA, 02421, USA
| | - Gang Sun
- Translate Bio, a Sanofi Company, Lexington, MA, 02421, USA.
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5
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Grozdanovic M, Samuel R, Grau B, Ansbro F. Serotype-specific quantification of residual free polysaccharide in multivalent pneumococcal conjugate vaccines. Glycoconj J 2024; 41:47-55. [PMID: 38224414 DOI: 10.1007/s10719-023-10143-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024]
Abstract
The Streptococcus pneumoniae bacteria has over 100 known serotypes that display a continuous change in prevalence by patients' age and geographical location and therefore necessitate continued efforts toward development of new vaccines with broader protection. Glycoconjugate vaccines have been instrumental in reducing global morbidity and mortality caused by Streptococcus pneumoniae infections. In these vaccines, the bacterial polysaccharide is conjugated to a carrier protein to enhance immunogenicity. To ensure well defined immunogenicity and stability of conjugated vaccines, reliable quantification of non-conjugated (free) polysaccharide is a critical, albeit challenging step during vaccine clinical dosing, release and stability monitoring. Multivalent preparations of Cross-reactive material 197 (CRM197)- conjugated pneumococcal polysaccharide materials often contain only nanogram levels of each individual free polysaccharide at final container concentrations. We have developed a novel method for the separation of free polysaccharides from conjugated material that requires no sample derivatization, employing instead an approach of quantitative immunoprecipitation of CRM197 with 3 different monoclonal antibodies and magnetic beads. A mix of antibodies against both linear and conformational epitopes enables successful removal of conjugates regardless of the protein folded state. The remaining free polysaccharide is subsequently measured in a serotype-specific ELISA.
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6
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Araki M, Kontani K. Analysis of the Guanine Nucleotide-Bound State of KRAS by Ion-Pair Reversed-Phase High-Performance Liquid Chromatography. Methods Mol Biol 2024; 2797:227-236. [PMID: 38570463 DOI: 10.1007/978-1-0716-3822-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Guanine nucleotides can be quantitatively analyzed by high-performance liquid chromatography (HPLC). Here we describe an ion-pair reversed-phase HPLC (IP-RP-HPLC)-based method, which enables analyzing GDP and GTP bound to small GTPases immunoprecipitated from cells. The activation status of FLAG-KRAS expressed in HEK293T cells can be investigated with the IP-RP-HPLC method. This method also can be adapted to determine the effects of compounds such as the KRAS/G12C inhibitor sotorasib on the activation status of FLAG-KRAS in the cells.
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Affiliation(s)
- Makoto Araki
- Department of Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
| | - Kenji Kontani
- Department of Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan.
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7
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Maier LP, Felix G, Fliegmann J. LuBiA (Luciferase-Based Binding Assay): Glowing Peptides as Sensitive Probes to Study Ligand-Receptor Interactions. Methods Mol Biol 2024; 2731:265-278. [PMID: 38019441 DOI: 10.1007/978-1-0716-3511-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The quantitative and qualitative biochemical description of molecular interactions is fundamental to the study of ligand/receptor pairs and their structure/function relationships. Bioactive peptides often are active at (sub-)nanomolar concentrations, indicating they have a high affinity for their sites of action, notably binding sites on receptors. Since such receptor proteins are commonly of low abundance, highly sensitive detection methods are required to study these ligand/receptor interactions. We present a protocol for an inexpensive luminescence-based detection setup in which the peptide ligand of interest is extended with the 11-amino acid HiBiT tag. This tag can be quantified easily down to fmol amounts by its ability to reconstitute the enzymatic activity of LgBiT, a truncated version of the Oplophorus gracilirostris luciferase.
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Affiliation(s)
- Louis-Philippe Maier
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Department of Plant Molecular Biology (DBMV), University of Lausanne, Lausanne, Switzerland
| | - Georg Felix
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Judith Fliegmann
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.
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8
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Kruglova N, Filatov A. Detecting PTP Protein-Protein Interactions by Fluorescent Immunoprecipitation Analysis (FIPA). Methods Mol Biol 2024; 2743:181-194. [PMID: 38147216 DOI: 10.1007/978-1-0716-3569-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Identifying protein-protein interactions is crucial for revealing protein functions and characterizing cellular processes. Manipulating PPIs has become widespread in treating human diseases such as cancer, autoimmunity, and infections. It has been recently applied to the regulation of protein tyrosine phosphatases (PTPs) previously considered undruggable. A broad panel of methods is available for studying PPIs. To complement the existing toolkit, we developed a simple method called fluorescent immunoprecipitation analysis (FIPA). This method is based on coimmunoprecipitation followed by protein gel electrophoresis and fluorescent imaging to visualize components of a protein complex simultaneously on a gel. The FIPA allows the detection of proteins expressed under native conditions and is compatible with mass spectrometry identification of protein bands.
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Affiliation(s)
- Natalia Kruglova
- Cell and Gene Technology Group, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, Russia
- National Research Center, Institute of Immunology of Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Alexander Filatov
- National Research Center, Institute of Immunology of Federal Medical Biological Agency of Russia, Moscow, Russia
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9
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Hinton SD. Understanding Pseudophosphatase Function Through Biochemical Interactions. Methods Mol Biol 2024; 2743:21-41. [PMID: 38147206 DOI: 10.1007/978-1-0716-3569-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Pseudophosphatases have been solidified as important signaling molecules that regulate signal transduction cascades. However, their mechanisms of action remain enigmatic. Reflecting this mystery, the prototypical pseudophosphatase STYX (phospho-serine-threonine/tyrosine-binding protein) was named with allusion to the river of the dead in Greek mythology to emphasize that these molecules are "dead" phosphatases. Although proteins with STYX domains do not catalyze dephosphorylation, this does not preclude their having other functions, including as integral elements of signaling networks. Thus, understanding their roles may mark them as potential novel drug targets. This chapter outlines common strategies used to characterize the functions of pseudophosphatases, using as an example MK-STYX [MAPK (mitogen-activated protein kinase) phospho-serine-threonine/tyrosine-binding], which has been linked to tumorigenesis, hepatocellular carcinoma, glioblastoma, apoptosis, and neuronal differentiation. We start with the importance of "restoring" (when possible) phosphatase activity in a pseudophosphatase, so the active mutant may be used as a comparison control throughout immunoprecipitation and mass spectrometry analyses. To this end, we provide protocols for site-directed mutagenesis, mammalian cell transfection, co-immunoprecipitation, phosphatase activity assays, and immunoblotting that we have used to investigate MK-STYX and the active mutant MK-STYXactive. We also highlight the importance of utilizing RNA interference (RNAi) "knockdown" technology to determine a cellular phenotype in various cell lines. Therefore, we outline our protocols for introducing short hairpin RNA (shRNA) expression plasmids into mammalian cells and quantifying knockdown of gene expression with real-time quantitative PCR (qPCR). We also provide a bioinformatic approach to investigating MK-STYX and MK-STYX(active mutant). These bioinformatic approaches can stand alone experimentally but also complement and enhance "wet" bench approaches such as binding assays and/or activity assays. A combination of cellular, molecular, biochemical, proteomic, and bioinformatic techniques has been a powerful tool in identifying novel functions of MK-STYX. Likewise, the information provided here should be a helpful guide to elucidating the functions of other pseudophosphatases.
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Affiliation(s)
- Shantá D Hinton
- Department of Biology, College of William and Mary, Williamsburg, VA, USA.
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10
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Guay KP, Ke H, Gierasch LM, Gershenson A, Hebert DN. Monitoring the Secretion and Activity of Alpha-1 Antitrypsin in Various Mammalian Cell Types. Methods Mol Biol 2024; 2750:143-163. [PMID: 38108975 PMCID: PMC10918612 DOI: 10.1007/978-1-0716-3605-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Overexpression of recombinant protein in mammalian cells is widely used for producing biologics, as protein maturation and post-translational modifications are similar to human cells. Some therapeutics, such as mRNA vaccines, target nonnative cells that may contain inefficient secretory machinery. For example, gene replacement therapies for alpha-1 antitrypsin (AAT), a glycoprotein normally produced in hepatocytes, are often targeted to muscle cells due to ease of delivery. In this chapter, we define methods for expressing AAT in representative cell types such as Huh-7; hepatocytes; Chinese hamster ovarian cells (CHO), a common host to produce biologics; and C2C12, a muscle progenitor cell line. Methods for metabolically labeling AAT to monitor secretion in these cell lines are described along with the use of proteostasis activators to increase the amount of AAT secreted in both C2C12 myoblasts and differentiated myotubes. Assays to assess the activity and glycan composition of overexpressed AAT are also presented. The usage of the proteostasis activator SAHA provided a 40% improvement in expression of active AAT in muscle-like cells and may be an advantageous adjuvant for recombinant production of proteins delivered by mRNA vaccines.
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Affiliation(s)
- Kevin P Guay
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Haiping Ke
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Daniel N Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA.
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA.
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11
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Fernandez-Olivares A, Retamal MA. Protocol for the Study of Connexin and DNA Interactions. Methods Mol Biol 2024; 2801:125-134. [PMID: 38578418 DOI: 10.1007/978-1-0716-3842-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Connexins (Cxs) are transmembrane proteins which form hemichannels and gap junction channels at the plasma membrane. These channels allow the exchange of ions and molecules between the intra- and extracellular space and between cytoplasm of adjacent cells, respectively. The channel function of Cx assemblies has been extensively studied; however, "noncanonical" functions have emerged in the last few decades and have capture the attentions of many researchers, including the role of some Cxs as gene modulators or transcription factors. In this chapter, we describe a protocol to study the interaction of Cx46 with DNA in HeLa cells. These methods can facilitate understanding the role of Cxs in physiological processes and pathological mechanisms, including, for example, the contribution of Cx46 in maintaining stemness of glioma cancer stem cells.
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Affiliation(s)
- Ainoa Fernandez-Olivares
- Programa de Comunicación Celular en Cáncer, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Mauricio A Retamal
- Programa de Comunicación Celular en Cáncer, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile.
- Programa de Comunicación Celular en Cáncer, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile.
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12
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Kim JS, Haimon Z, Boura-Halfon S, Jung S. Translatome Profiling of Tissue-Resident Macrophages Using the RiboTag Approach. Methods Mol Biol 2024; 2713:253-267. [PMID: 37639128 DOI: 10.1007/978-1-0716-3437-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Global gene expression profiling has provided valuable insights into the specific contributions of different cell types to various physiological processes. Notably though, both bulk and single-cell transcriptomics require the prior retrieval of the cells from their tissue context to be analyzed. Isolation protocols for tissue macrophages are, however, notoriously inefficient and, moreover, prone to introduce considerable bias and artifacts. Here, we will discuss a valuable alternative, originally introduced by Amieux and colleagues. This so-called RiboTag approach allows, in combination with respective macrophage-specific Cre transgenic lines, to retrieve macrophage translatomes from crude tissue extracts. We will review our experience with this ingenious method, focusing on the study of brain macrophages, including microglia and border-associated cells. We will elaborate on the advantages of the RiboTag approach that render it a valuable complement to standard cell sorting-based profiling strategies, especially for the investigation of tissue macrophages.
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Affiliation(s)
- Jung-Seok Kim
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Zhana Haimon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sigalit Boura-Halfon
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Jung
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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13
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D'Ippolito RA, Scheidemantle GM, Smith BP, Powell K, Eury S, Neish A, Mehalko J, Beaumont L, Fer N, Wall V, Burgan W, Maciag AE, Esposito D, DeHart CJ. FLAG-KRAS4B as a Model System for KRAS4B Proteoform and PTM Evaluation by Mass Spectrometry. Methods Mol Biol 2024; 2797:299-322. [PMID: 38570469 DOI: 10.1007/978-1-0716-3822-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Prior analysis of intact and modified protein forms (proteoforms) of KRAS4B isolated from cell lines and tumor samples by top-down mass spectrometry revealed the presence of novel posttranslational modifications (PTMs) and potential evidence of context-specific KRAS4B modifications. However, low endogenous proteoform signal resulted in ineffective characterization, making it difficult to visualize less abundant PTMs or perform follow-up PTM validation using standard proteomic workflows. The NCI RAS Initiative has developed a model system, whereby KRAS4B bearing an N-terminal FLAG tag can be stably expressed within a panel of cancer cell lines. Herein, we present a method for combining immunoprecipitation with complementary proteomic methods to directly analyze N-terminally FLAG-tagged KRAS4B proteoforms and PTMs. We provide detailed protocols for FLAG-KRAS4B purification, proteoform analysis by targeted top-down LC-MS/MS, and validation of abundant PTMs by bottom-up LC-MS/MS with example results.
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Affiliation(s)
- Robert A D'Ippolito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Grace M Scheidemantle
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brian P Smith
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Katie Powell
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott Eury
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Abigail Neish
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jennifer Mehalko
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lauren Beaumont
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nicole Fer
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vanessa Wall
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William Burgan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anna E Maciag
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Caroline J DeHart
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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Medina-Puche L, Lozano-Durán R. Immunoprecipitation Followed by Mass Spectrometry: An Approach for Identifying Host-Viral Protein-Protein Interactions. Methods Mol Biol 2024; 2724:289-305. [PMID: 37987914 DOI: 10.1007/978-1-0716-3485-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
As obligate intracellular parasites, viruses rely on the efficient manipulation of the cell they invade in order to multiply and spread. Protein-protein interactions between viral proteins (or their complexes) and cellular proteins are at the interface between virus and host and hence crucial for the outcome of the infection. Multiple techniques can be used to study protein-protein interactions in vivo in the context of the infected cell; among them, immunoprecipitation followed by mass spectrometry (IP-MS) has proven an efficient approach for the unbiased identification of protein complexes containing a viral protein of interest. In this chapter, we discuss how to employ IP-MS to define the interactome of plant virus proteins by using transient expression in the experimental host Nicotiana benthamiana, using the geminivirus tomato yellow leaf curl virus (TYLCV) as an example.
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Affiliation(s)
- Laura Medina-Puche
- Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany
| | - Rosa Lozano-Durán
- Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany.
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15
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Metwally H, Elbrashy MM. Analysis of Protein Interactions in Patient-Derived Xenografts Using Immunoprecipitation. Methods Mol Biol 2024; 2806:219-227. [PMID: 38676806 DOI: 10.1007/978-1-0716-3858-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Proteins are large, complex molecules that regulate multiple functions within the cell. The protein rarely functions as a single molecule, but rather interacts with one or more other proteins forming a dynamic network. Protein-protein interactions are critical for regulating the cell's response toward various stimuli from outside and inside the cell. Identification of protein-protein interactions enhanced our understanding of various biological processes in the living cell. Immunoprecipitation (IP) has been one of the standard and most commonly used biochemical methods to identify and confirm protein-protein interactions. IP uses a target protein-specific antibody conjugated with protein A/G affinity beads to identify molecules interacting with the target protein. Here, we describe the principle, procedure and challenges of the IP assay.
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Affiliation(s)
- Hozaifa Metwally
- Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, Osaka, Japan.
| | - Maha M Elbrashy
- Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Biochemistry Department, Biotechnology Research Institute, National Research Center, Giza, Egypt
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16
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Andrabi SBA, Batkulwar K, Bhosale SD, Moulder R, Khan MH, Buchacher T, Khan MM, Arnkil I, Rasool O, Marson A, Kalim UU, Lahesmaa R. HIC1 interacts with FOXP3 multi protein complex: Novel pleiotropic mechanisms to regulate human regulatory T cell differentiation and function. Immunol Lett 2023; 263:123-132. [PMID: 37838026 DOI: 10.1016/j.imlet.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/16/2023]
Abstract
Transcriptional repressor, hypermethylated in cancer 1 (HIC1) participates in a range of important biological processes, such as tumor repression, immune suppression, embryonic development and epigenetic gene regulation. Further to these, we previously demonstrated that HIC1 provides a significant contribution to the function and development of regulatory T (Treg) cells. However, the mechanism by which it regulates these processes was not apparent. To address this question, we used affinity-purification mass spectrometry to characterize the HIC1 interactome in human Treg cells. Altogether 61 high-confidence interactors were identified, including IKZF3, which is a key transcription factor in the development of Treg cells. The biological processes associated with these interacting proteins include protein transport, mRNA processing, non-coding (ncRNA) transcription and RNA metabolism. The results revealed that HIC1 is part of a FOXP3-RUNX1-CBFB protein complex that regulates Treg signature genes thus improving our understanding of HIC1 function during early Treg cell differentiation.
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Affiliation(s)
- Syed Bilal Ahmad Andrabi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Kedar Batkulwar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Tanja Buchacher
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Ilona Arnkil
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; InFLAMES Research Flagship Center, University of Turku; Institute of Biomedicine, University of Turku.
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Barman P, Kaja A, Chakraborty P, Bhaumik SR. Chromatin and non-chromatin immunoprecipitations to capture protein-protein and protein-nucleic acid interactions in living cells. Methods 2023; 218:158-166. [PMID: 37611837 PMCID: PMC10528071 DOI: 10.1016/j.ymeth.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023] Open
Abstract
Proteins are expressed from genes via sequential biological processes of transcription, mRNA processing, export and translation, and play their roles in maintaining cellular functions via interactions with proteins, DNAs or RNAs. Thus, it is important to study the protein interactions during biological processes in living cells towards understanding their mechanisms-of-action in real time. Methodologies have been developed over the years to study protein interactions in vivo. One state-of-the-art approach is formaldehyde crosslinking-based immuno- or chemi-precipitation to analyze selective as well as genome/proteome-wide interactions in living cells. It is a popular and widely used methodology for cellular analysis of the protein-protein and protein-nucleic acid interactions. Here, we describe this approach to analyze protein-protein/nucleic acid interactions in vivo.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Amala Kaja
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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18
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Cortázar MA, Fong N, Bentley DL. Genome-wide Mapping of 5'-monophosphorylated Ends of Mammalian Nascent RNA Transcripts. Bio Protoc 2023; 13:e4828. [PMID: 37753464 PMCID: PMC10518774 DOI: 10.21769/bioprotoc.4828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 09/28/2023] Open
Abstract
In eukaryotic cells, RNA biogenesis generally requires processing of the nascent transcript as it is being synthesized by RNA polymerase. These processing events include endonucleolytic cleavage, exonucleolytic trimming, and splicing of the growing nascent transcript. Endonucleolytic cleavage events that generate an exposed 5'-monophosphorylated (5'-PO4) end on the growing nascent transcript occur in the maturation of rRNAs, tRNAs, and mRNAs. These 5'-PO4 ends can be a target of further processing or be subjected to 5'-3' exonucleolytic digestion that may result in termination of transcription. Here, we describe how to identify 5'-PO4 ends of intermediates in nascent RNA metabolism. We capture these species via metabolic labeling with bromouridine followed by immunoprecipitation and specific ligation of 5'-PO4 RNA ends with the 3'-hydroxyl group of a 5' adaptor (5'-PO4 Bru-Seq) using RNA ligase I. These ligation events are localized at single nucleotide resolution via highthroughput sequencing, which identifies the position of 5'-PO4 groups precisely. This protocol successfully detects the 5'monophosphorylated ends of RNA processing intermediates during production of mature ribosomal, transfer, and micro RNAs. When combined with inhibition of the nuclear 5'-3' exonuclease Xrn2, 5'-PO4 Bru-Seq maps the 5' splice sites of debranched introns and mRNA and tRNA 3' end processing sites cleaved by CPSF73 and RNaseZ, respectively. Key features • Metabolic labeling for brief periods with bromouridine focuses the analysis of 5'-PO4 RNA ends on the population of nascent transcripts that are actively transcribed. • Detects 5'-PO4 RNA ends on nascent transcripts produced by all RNA polymerases. • Detects 5'-PO4 RNA ends at single nucleotide resolution.
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Affiliation(s)
- Michael A. Cortázar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - David L. Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
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Hayden H, Klopf J, Ibrahim N, Knöbl V, Sotir A, Mekis R, Nowikovsky K, Eilenberg W, Neumayer C, Brostjan C. Quantitation of oxidized nuclear and mitochondrial DNA in plasma samples of patients with abdominal aortic aneurysm. Free Radic Biol Med 2023; 206:94-105. [PMID: 37353175 DOI: 10.1016/j.freeradbiomed.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023]
Abstract
There is accumulating evidence that pro-inflammatory features are inherent to mitochondrial DNA and oxidized DNA species. 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) is the most frequently studied oxidatively generated lesion. Modified DNA reaches the circulation upon cell apoptosis, necrosis or neutrophil extracellular trap (NET) formation. Standard chromatography-based techniques for the assessment of 8-oxodGuo imply degradation of DNA to a single base level, thus precluding the attribution to a nuclear or mitochondrial origin. We therefore aimed to establish a protocol for the concomitant assessment of oxidized mitochondrial and nuclear DNA from human plasma samples. We applied immunoprecipitation (IP) for 8-oxodGuo to separate oxidized from non-oxidized DNA species and subsequent quantitative polymerase chain reaction (qPCR) to assign them to their subcellular source. The IP procedure failed when applied directly to plasma samples, i.e. isotype control precipitated similar amounts of DNA as the specific 8-oxodGuo antibody. In contrast, DNA isolation from plasma prior to the IP process provided assay specificity with little impact on DNA oxidation status. We further optimized sensitivity and efficiency of qPCR analysis by reducing amplicon length and targeting repetitive nuclear DNA elements. When the established protocol was applied to plasma samples of abdominal aortic aneurysm (AAA) patients and control subjects, the AAA cohort displayed significantly elevated circulating non-oxidized and total nuclear DNA and a trend for increased levels of oxidized mitochondrial DNA. An enrichment of mitochondrial versus nuclear DNA within the oxidized DNA fraction was seen for AAA patients. Regarding the potential source of circulating DNA, we observed a significant correlation of markers of neutrophil activation and NET formation with nuclear DNA, independent of oxidation status. Thus, the established method provides a tool to detect and distinguish the release of oxidized nuclear and mitochondrial DNA in human plasma and offers a refined biomarker to monitor disease conditions of pro-inflammatory cell and tissue destruction.
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Affiliation(s)
- Hubert Hayden
- Department of General Surgery, Division of Vascular Surgery, Medical University of Vienna and University Hospital Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Johannes Klopf
- Department of General Surgery, Division of Vascular Surgery, Medical University of Vienna and University Hospital Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Nahla Ibrahim
- Department of General Surgery, Division of Vascular Surgery, Medical University of Vienna and University Hospital Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Viktoria Knöbl
- Department of General Surgery, Division of Vascular Surgery, Medical University of Vienna and University Hospital Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Anna Sotir
- Department of General Surgery, Division of Vascular Surgery, Medical University of Vienna and University Hospital Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Ronald Mekis
- Institute of Physiology, Pathophysiology and Biophysics, Unit of Physiology and Biophysics, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Karin Nowikovsky
- Institute of Physiology, Pathophysiology and Biophysics, Unit of Physiology and Biophysics, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Wolf Eilenberg
- Department of General Surgery, Division of Vascular Surgery, Medical University of Vienna and University Hospital Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Christoph Neumayer
- Department of General Surgery, Division of Vascular Surgery, Medical University of Vienna and University Hospital Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Christine Brostjan
- Department of General Surgery, Division of Vascular Surgery, Medical University of Vienna and University Hospital Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
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20
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Nguyen TP, Nguyen BT, Dao TNL, Ho TH, Lee PT. Investigation of the functional role of UNC93B1 in Nile tilapia (Oreochromis niloticus): mRNA expression, subcellular localization, and physical interaction with fish-specific TLRs. Fish Shellfish Immunol 2023; 139:108902. [PMID: 37330026 DOI: 10.1016/j.fsi.2023.108902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/19/2023]
Abstract
Nile tilapia (Oreochromis niloticus) is one of the major food fish worldwide. The farming business, on the other hand, has faced considerable obstacles, such as disease infestations. Toll-like receptors (TLRs) play an important function in the activation of the innate immune system in response to infections. Unc-93 homolog B1 (UNC93B1) is a key regulator of nucleic acid (NA)-sensing TLRs. Here the UNC93B1 gene, which was cloned from Nile tilapia tissue for this investigation, had the same genetic structure as a homologous gene in humans and mice. Phylogenetic analysis revealed that Nile tilapia UNC93B1 clustered with UNC93B1 from other species and separately from the UNC93A clade. The gene structure of the Nile tilapia UNC93B1 was found to be identical to that of human UNC93B1. Our gene expression studies revealed that Nile tilapia UNC93B1 was highly expressed in the spleen, followed by other immune-related tissues such as the head kidney, gills, and intestine. Moreover, Nile tilapia UNC93B1 mRNA transcripts were up-regulated in vivo in the head kidney and spleen tissues from poly I:C and Streptococcus agalactiae injected Nile tilapia, as well as in vitro in LPS stimulated Tilapia head kidney (THK) cells. The Nile tilapia UNC93B1-GFP protein signal was detected in the cytosol of THK cells and was co-localized with endoplasmic reticulum and lysosome but not with mitochondria. Moreover, the results of a co-immunoprecipitation and immunostaining analysis showed that Nile tilapia UNC93B1 can be pulled down with fish-specific TLRs such as TLR18 and TLR25 from Nile tilapia, and was found to be co-localized with these fish-specific TLRs in the THK cells. Overall, our findings highlight the potential role of UNC93B1 as an accessory protein in fish-specific TLR signaling.
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Affiliation(s)
- Tan Phat Nguyen
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Bao Trung Nguyen
- College of Aquaculture and Fisheries, Can Tho University, Viet Nam
| | - Thi Ngoc Linh Dao
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Thi Hang Ho
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Po-Tsang Lee
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan.
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21
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Peerapen P, Boonmark W, Thongboonkerd V. Characterizations of annexin A1-interacting proteins in apical membrane and cytosolic compartments of renal tubular epithelial cells. Comput Struct Biotechnol J 2023; 21:3796-3809. [PMID: 37560129 PMCID: PMC10407547 DOI: 10.1016/j.csbj.2023.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Annexin A1 (ANXA1) is a multifunctional calcium-binding protein that can bind to membrane phospholipids. Under high-calcium condition, ANXA1 expression increases on renal epithelial cell surface, leading to enhanced adhesion of calcium oxalate (CaOx) crystal (stone material) onto the cells. To regulate various cellular processes, ANXA1 interacts with many other intracellular protein partners. However, components of the ANXA1-interacting protein complex remain unclear. Herein, we characterized the interacting complexes of apical membrane (ApANXA1) and cytosolic (cyANXA1) forms of ANXA1 in apical membrane and cytosolic compartments, respectively, of renal epithelial cells under high-calcium condition using proteomic and bioinformatic approaches. After fractionation, the ApANXA1- and CyANXA1-interacting partners were identified by immunoprecipitation followed by nanoLC‑ESI‑Qq-TOF tandem mass spectrometry (IP-MS/MS). The ANXA1-interacting partners that were common in both apical membrane and cytosolic compartments and those unique in each compartment were then analyzed for their physico-chemical properties (molecular weight, isoelectric point, amino acid contents, instability index, aliphatic index, and grand average of hydropathicity), secondary structure (α-helix, β-turn, random coil, and extended strand), molecular functions, biological processes, reactome pathways and KEGG pathways. The data demonstrated that each set of these interacting proteins exhibited common and unique characteristics and properties. The knowledge from this study may lead to better understanding of the ApANXA1 and CyAXNA1 biochemistry and functions as well as the pathophysiology of CaOx kidney stone formation induced by high-calcium condition.
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Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanida Boonmark
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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Miske R, Scharf M, Borowski K, Rieckhoff N, Teegen B, Denno Y, Probst C, Guthke K, Didrihsone I, Wildemann B, Ruprecht K, Komorowski L, Jarius S. Septin-3 autoimmunity in patients with paraneoplastic cerebellar ataxia. J Neuroinflammation 2023; 20:88. [PMID: 36997937 PMCID: PMC10061979 DOI: 10.1186/s12974-023-02718-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/03/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Septins are cytoskeletal proteins with filament forming capabilities, which have multiple roles during cell division, cellular polarization, morphogenesis, and membrane trafficking. Autoantibodies against septin-5 are associated with non-paraneoplastic cerebellar ataxia, and autoantibodies against septin-7 with encephalopathy with prominent neuropsychiatric features. Here, we report on newly identified autoantibodies against septin-3 in patients with paraneoplastic cerebellar ataxia. We also propose a strategy for anti-septin autoantibody determination. METHODS Sera from three patients producing similar immunofluorescence staining patterns on cerebellar and hippocampal sections were subjected to immunoprecipitation followed by mass spectrometry. The identified candidate antigens, all of which were septins, were expressed recombinantly in HEK293 cells either individually, as complexes, or combinations missing individual septins, for use in recombinant cell-based indirect immunofluorescence assays (RC-IIFA). Specificity for septin-3 was further confirmed by tissue IIFA neutralization experiments. Finally, tumor tissue sections were analyzed immunohistochemically for septin-3 expression. RESULTS Immunoprecipitation with rat cerebellum lysate revealed septin-3, -5, -6, -7, and -11 as candidate target antigens. Sera of all three patients reacted with recombinant cells co-expressing septin-3/5/6/7/11, while none of 149 healthy control sera was similarly reactive. In RC-IIFAs the patient sera recognized only cells expressing septin-3, individually and in complexes. Incubation of patient sera with five different septin combinations, each missing one of the five septins, confirmed the autoantibodies' specificity for septin-3. The tissue IIFA reactivity of patient serum was abolished by pre-incubation with HEK293 cell lysates overexpressing the septin-3/5/6/7/11 complex or septin-3 alone, but not with HEK293 cell lysates overexpressing septin-5 as control. All three patients had cancers (2 × melanoma, 1 × small cell lung cancer), presented with progressive cerebellar syndromes, and responded poorly to immunotherapy. Expression of septin-3 was demonstrated in resected tumor tissue available from one patient. CONCLUSIONS Septin-3 is a novel autoantibody target in patients with paraneoplastic cerebellar syndromes. Based on our findings, RC-IIFA with HEK293 cells expressing the septin-3/5/6/7/11 complex may serve as a screening tool to investigate anti-septin autoantibodies in serological samples with a characteristic staining pattern on neuronal tissue sections. Autoantibodies against individual septins can then be confirmed by RC-IIFA expressing single septins.
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Affiliation(s)
- Ramona Miske
- Institute for Experimental Immunology, affiliated to EUROIMMUN AG, Lübeck, Germany
| | - Madeleine Scharf
- Institute for Experimental Immunology, affiliated to EUROIMMUN AG, Lübeck, Germany.
| | - Kathrin Borowski
- Clinical Immunological Laboratory Prof. Dr. med. Winfried Stöcker, Lübeck, Germany
| | - Nicole Rieckhoff
- Institute for Experimental Immunology, affiliated to EUROIMMUN AG, Lübeck, Germany
| | - Bianca Teegen
- Clinical Immunological Laboratory Prof. Dr. med. Winfried Stöcker, Lübeck, Germany
| | - Yvonne Denno
- Institute for Experimental Immunology, affiliated to EUROIMMUN AG, Lübeck, Germany
| | - Christian Probst
- Institute for Experimental Immunology, affiliated to EUROIMMUN AG, Lübeck, Germany
| | - Kersten Guthke
- Department of Neurology, Städtisches Klinikum Görlitz, Görlitz, Germany
| | - Ieva Didrihsone
- Department of Neurology, Hermann-Josef-Krankenhaus, Erkelenz, Germany
| | - Brigitte Wildemann
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | - Klemens Ruprecht
- Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lars Komorowski
- Institute for Experimental Immunology, affiliated to EUROIMMUN AG, Lübeck, Germany
| | - Sven Jarius
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Heidelberg, Germany.
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23
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Aufschnaiter A, Carlström A, Ott M. Yeast Mitoribosome Purification and Analyses by Sucrose Density Centrifugation and Immunoprecipitation. Methods Mol Biol 2023; 2661:119-132. [PMID: 37166635 DOI: 10.1007/978-1-0716-3171-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mitochondrial protein biosynthesis is maintained by an interplay between the mitochondrial ribosome (mitoribosome) and a large set of protein interaction partners. This interactome regulates a diverse set of functions, including mitochondrial gene expression, translation, protein quality control, and respiratory chain assembly. Hence, robust methods to biochemically and structurally analyze this molecular machinery are required to understand the sophisticated regulation of mitochondrial protein biosynthesis. In this chapter, we present detailed protocols for immunoprecipitation, sucrose cushions, and linear sucrose gradients to purify and analyze mitoribosomes and their interaction partners.
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Affiliation(s)
- Andreas Aufschnaiter
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden.
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24
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Lo Sardo F. Co- Immunoprecipitation (Co-Ip) in Mammalian Cells. Methods Mol Biol 2023; 2655:67-77. [PMID: 37212989 DOI: 10.1007/978-1-0716-3143-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The cell is a fantastic place where molecules dynamically move through the various cellular structures and compartments and meet each other, either transiently or in more stable complexes. These complexes have always a specific biological function; thus, it is important to identify and characterize the interaction between molecules, either DNA/RNA, DNA/DNA, protein/DNA, protein/protein, and so on. polycomb group proteins (PcG proteins) are epigenetic repressors involved in important physiologic processes as development and differentiation. They act on the chromatin through the formation of a repressive environment involving histone modification, recruitment of co-repressors, and chromatin-chromatin interactions. PcG form multiprotein complexes, whose characterization required several approaches. In this chapter, I will describe the co-immunoprecipitation (Co-IP) protocol, an easy method used to identify and analyze multiprotein complexes. In Co-IP, an antibody is used to isolate its target antigen, along with its binding partners, from a mixed sample. The binding partners purified with the immunoprecipitated protein can be identified by Western blot or by mass spectrometry.
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Affiliation(s)
- Federica Lo Sardo
- IRCCS Regina Elena National Cancer Institute, UOC ricerca traslazionale oncologica, Rome, Italy.
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25
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Kell M, Halpern A, Fölsch H. Immunoprecipitation and Western Blot Analysis of AP-1 Clathrin-Coated Vesicles. Methods Mol Biol 2023; 2557:619-633. [PMID: 36512241 DOI: 10.1007/978-1-0716-2639-9_37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The function and integrity of epithelial cells depends on the polarized localization of transmembrane proteins at either apical or basolateral plasma membrane domains. To facilitate sorting to the basolateral domain, columnar epithelial cells express the tissue-specific AP-1B complex in addition to the ubiquitously expressed AP-1A. Both AP-1A and AP-1B are heterotetrameric clathrin adaptor protein complexes that are closely related. Here we describe a biochemical method to separate AP-1B from AP-1A clathrin-coated vesicles by immunoprecipitation from clathrin-coated vesicle pellets that were obtained by ultracentrifugation and analyzed by SDS-PAGE and western blot using fluorescently labeled secondary antibodies.
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Affiliation(s)
- Margaret Kell
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Abby Halpern
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Heike Fölsch
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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26
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Smaczniak C. Immunoprecipitation-Mass Spectrometry (IP-MS) of Protein-Protein Interactions of Nuclear-Localized Plant Proteins. Methods Mol Biol 2023; 2698:163-181. [PMID: 37682475 DOI: 10.1007/978-1-0716-3354-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Transcription factors that act within a gene regulatory network (GRN) often interact with other proteins such as chromatin remodeling factors, histone modifiers, and other co-regulators. Characterizing these interactions is crucial for understanding the function and mechanism of action of a transcription factor. Here, a method for the identification of protein-protein interactions of nuclear-localized, transcription-associated factors is described. The method is based on the immunoprecipitation (IP) of a fluorophore-tagged target, followed by mass spectrometry (MS), peptide identification, and quantification of interacting proteins. By applying label-free quantification to IPs and their input protein extracts, statistically controlled protein enrichment ratios uncover high-confidence interaction partners of the target. A complete step-by-step procedure, including sample preparation, MS settings, data analysis, and visualization is provided.
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Affiliation(s)
- Cezary Smaczniak
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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27
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Renaud MS, Seroussi U, Claycomb JM. Analysis of C. elegans Germline Small RNA Pathways. Methods Mol Biol 2023; 2677:37-59. [PMID: 37464234 DOI: 10.1007/978-1-0716-3259-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Sequence-specific gene regulation by small RNA (sRNA) pathways is essential for the development and function of organisms in all domains of life. These regulatory complexes, containing an Argonaute protein (AGO) guided by a bound sRNA, have the potential to regulate thousands of individual target transcripts at both the co- and post-transcriptional level. Determining the repertoire of transcripts that an AGO is capable of regulating in a particular context is essential to understanding the function of these regulatory modules. Immunoprecipitation (IP) of AGOs and subsequent RNA sequencing of their bound sRNAs allows for the inference of their target transcripts by mapping the sequences of the co-precipitated sRNAs back to their complementary target transcripts. This approach can be complemented by sequencing sRNAs from ago mutants as sRNA transcripts are degraded in the absence of their AGO binding partner. Here, we describe a framework for analyzing AGO/sRNA pathways in the germline, from using CRISPR-Cas9 to tag or mutate AGOs, through protocols for the extraction, sequencing, and analysis of sRNAs from AGO IPs and ago mutants.
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Affiliation(s)
- Mathias S Renaud
- Department of Molecular Genetics, University of Toronto, Toronto, ON, USA
| | - Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, USA
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, USA.
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28
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Worboys JD, Palazón-Riquelme P, López-Castejón G. Method to Measure Ubiquitination of NLRs. Methods Mol Biol 2023; 2696:105-114. [PMID: 37578718 DOI: 10.1007/978-1-0716-3350-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Posttranslational modifications are crucial in determining the functions of proteins in the cell. Modification of the NLRP3 inflammasome by the ubiquitin system has recently emerged as a new level of regulation of the inflammasome complex. Here we describe a method to detect poly-ubiquitination of NRLP3 using two different approaches: (i) detection with a ubiquitin antibody or (ii) using TUBEs (Tandem Ubiquitin Binding entities). This approach can be used to detect ubiquitination of other NLRs or other proteins.
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Affiliation(s)
- Jonathan D Worboys
- Manchester Collaborative Centre of Inflammation Research, Faculty of Life Sciences, The University of Manchester, Manchester, UK
| | - Pablo Palazón-Riquelme
- Manchester Collaborative Centre of Inflammation Research, Faculty of Life Sciences, The University of Manchester, Manchester, UK
| | - Gloria López-Castejón
- Manchester Collaborative Centre of Inflammation Research, Faculty of Life Sciences, The University of Manchester, Manchester, UK.
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29
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Pang HW, Barrientos A. Rapid Cryopurification of the Yeast Mitochondrial Ribosome. Methods Mol Biol 2023; 2661:133-141. [PMID: 37166636 PMCID: PMC10654548 DOI: 10.1007/978-1-0716-3171-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cryogenic milling, or cryomilling, involves the use of liquid nitrogen to lower the temperature of the biological material and/or the milling process. When applied to the study of subcellular or suborganellar structures and processes, it allows for their rapid extraction from whole cells frozen in the physiological state of choice. This approach has proven to be useful for the study of yeast mitochondrial ribosomes. Following cryomilling of 100 mL of yeast culture, conveniently tagged mitochondrial ribosomes can be immunoprecipitated and purified in native conditions. These ribosomes are suitable for the application of downstream approaches. These include mitoribosome profiling to analyze the mitochondrial translatome or mass spectrometry analyses to assess the mitoribosome proteome in normal growth conditions or under stress, as described in this method.
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Affiliation(s)
- Hong Weng Pang
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
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30
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Law J, Günther S, Watanabe S. Epitranscriptome Mapping of N 6-Methyladenosine Using m 6A Immunoprecipitation with High Throughput Sequencing in Skeletal Muscle Stem Cells. Methods Mol Biol 2023; 2640:431-443. [PMID: 36995611 DOI: 10.1007/978-1-0716-3036-5_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
N6-Methyladenosine (m6A), one of the most abundant chemical modifications in mRNA (epitranscriptome), contributes to the regulation of biological processes by iterating gene expression post-transcriptionally. A number of publications on m6A modification have escalated in the recent past, due to the advancements in profiling m6A along the transcriptome using different approaches. The vast majority of studies primarily focused on m6A modification on cell lines but not primary cells. We present in this chapter a protocol for m6A immunoprecipitation with high throughput sequencing (MeRIP-Seq) that profiles m6A on mRNA with merely 100 μg total RNA worth of muscle stem cells as starting material. With this MeRIP-Seq, we observed epitranscriptome landscape in muscle stem cells.
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Affiliation(s)
- Justin Law
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research (W.G Kerckhoff-Institute), Bad Nauheim, Germany
| | - Stefan Günther
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research (W.G Kerckhoff-Institute), Bad Nauheim, Germany
| | - Shuichi Watanabe
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research (W.G Kerckhoff-Institute), Bad Nauheim, Germany.
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31
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Muneta-Arrate I, Diez-Alarcia R. [ 35S]GTPγS (Guanosine-5'-O-(γ-thio)triphosphate-[ 35S]) Binding Scintillation Proximity Assay Experiments in Postmortem Brain Tissue. Methods Mol Biol 2023; 2687:31-43. [PMID: 37464160 DOI: 10.1007/978-1-0716-3307-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) are the very first effector in signal transduction events triggered by G-protein-coupled receptors (GPCRs). One of the most widely used approaches for determining GPCR activity in native tissue is based on the binding of [35S]GTPγS. Classically, an heterogeneous procedure including a filtration step has been used, but a modification of the protocol including an immunoprecipitation step has allowed the specific discrimination of the contribution of the different Gα subunit subtypes to the effect of each ligand. Nowadays, that the concept of functional selectivity has been demonstrated for several ligands and GPCRs, information obtained from this methodological approach will be very useful for broadening the knowledge of GPCRs signaling profiles and describing the effect of different ligands over them. In this chapter we will describe the detailed protocol of antibody-capture [35S]GTPγS scintillation proximity assay (SPA) in order to provide the reader with comprehensive guidelines to study receptor-mediated functional activation of different Gα-protein subtypes in native mammalian brain membranes. In addition, advantages and limitations of this method will be described, as well as future direction in the application of this approach indicated.
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Affiliation(s)
- I Muneta-Arrate
- Department of Pharmacology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Bizkaia, Spain
| | - R Diez-Alarcia
- Department of Pharmacology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain.
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Bizkaia, Spain.
- Biocruces Bizkaia Health Research Institute, Bizkaia, Spain.
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32
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Kahiapo JK, Monahan K. Chromatin Immunoprecipitation from Formaldehyde Cross-Linked Olfactory Sensory Neurons. Methods Mol Biol 2023; 2710:71-82. [PMID: 37688725 DOI: 10.1007/978-1-0716-3425-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Abstract
Chromatin immunoprecipitation (ChIP) allows a researcher to determine the genomic occupancy of nuclear proteins, providing insight into the roles of transcription factors, chromatin modifiers, histone modifications, and other factors bound to DNA. Protein-DNA interactions are first fixed in vivo by chemical cross-linking, and then a target protein is captured together with any associated DNA by an antibody mediated pull-down. The co-immunoprecipitated DNA can then be assayed by quantitative PCR or deep sequencing. Here, we demonstrate this technique using murine olfactory sensory neurons (OSNs) purified using fluorescence-activated cell sorting (FACS) and antibodies for the ubiquitous chromatin protein CTCF.
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Affiliation(s)
- Jerome K Kahiapo
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Kevin Monahan
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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33
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Hino S, Sato T, Nakao M. Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers. Methods Mol Biol 2023; 2577:55-64. [PMID: 36173565 DOI: 10.1007/978-1-0716-2724-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the most widely used method for analyzing genome-wide DNA-protein interactions. Because there is considerable variation in the modes and strengths of DNA-protein interactions, chromatin immunoprecipitation (ChIP) protocols have been diversified and optimized for different needs. Here, we describe protocols for detecting histone modifications and modifiers using various crosslinking and immunoprecipitation conditions. We provide a complete ChIP-seq workflow covering sample preparation, immunoprecipitation, next-generation sequencing (NGS) library preparation, and data analyses.
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Affiliation(s)
- Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan.
| | - Tetsuya Sato
- Research Laboratory, H.U. Group Research Institute G.K., Tokyo, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan.
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34
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Kim IV, Demtröder T, Kuhn CD. Isolation and Library Preparation of Planarian piRNAs. Methods Mol Biol 2023; 2680:29-54. [PMID: 37428369 DOI: 10.1007/978-1-0716-3275-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In planarian flatworms, piRNAs and SMEDWI (Schmidtea mediterranea PIWI) proteins are both essential for the animals' impressive regenerative ability and for their survival. A knockdown of SMEDWI proteins disrupts the specification of the planarian germline and impairs stem cell differentiation, resulting in lethal phenotypes. As the molecular targets of PIWI proteins and thus their biological function are determined by PIWI-bound small RNAs, termed piRNAs (for PIWI-interacting RNAs), it is imperative to study the wealth of PIWI-bound piRNAs using next-generation sequencing-based techniques. Prior to sequencing, piRNAs bound to individual SMEDWI proteins must be isolated. To that end, we established an immunoprecipitation protocol that can be applied to all planarian SMEDWI proteins. Co-immunoprecipitated piRNAs are visualized by using qualitative radioactive 5'-end labeling, which detects even trace amounts of small RNAs. Next, isolated piRNAs are subjected to a library preparation protocol that has been optimized for the efficient capture of piRNAs, whose 3'-ends carry a 2'-O-methyl modification. Successfully prepared piRNA libraries are subjected to Illumina-based next-generation sequencing. Obtained data are analyzed as presented in the accompanying manuscript.
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Affiliation(s)
- Iana V Kim
- RNA Biochemistry, University of Bayreuth, Bayreuth, Germany
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Tim Demtröder
- RNA Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Claus-D Kuhn
- RNA Biochemistry, University of Bayreuth, Bayreuth, Germany.
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35
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Wang L, Sanchez J, Hess D, Matthias P. Immunoprecipitation of HDAC6 and Interacting Proteins. Methods Mol Biol 2023; 2589:493-508. [PMID: 36255645 DOI: 10.1007/978-1-0716-2788-4_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The lysine deacetylase HDAC6 has unique structural and functional properties: It contains tandem catalytic domains that can deacetylate a variety of proteins and a zinc finger domain that binds ubiquitin. HDAC6 has been implicated in a variety of biological processes, normal or pathological, such as cellular motility, stress response, cancer, neurodegeneration, or viral infection. Due to this, HDAC6 is considered an attractive therapeutic target, and there is a major interest to identify small molecule inhibitors. To gain a mechanistic understanding of how HDAC6 impacts these different biological processes, there is a continued need to discover additional substrates as well as interacting proteins in different paradigms. One approach to achieve this is to perform HDAC6 immunoprecipitations to identify partner proteins. We describe here our optimized protocols to immunoprecipitate HDAC6 with the goal to identify or validate interacting proteins.
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Affiliation(s)
- Longlong Wang
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jacint Sanchez
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Sciences, University of Basel, Basel, Switzerland.
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36
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Casagrande F, Serino G. Immunoprecipitation of Cullin-Ring Ligases (CRLs) in Arabidopsis thaliana Seedlings. Methods Mol Biol 2023; 2581:31-42. [PMID: 36413308 DOI: 10.1007/978-1-0716-2784-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
CRL (Cullin-Ring ubiquitin ligases) are the major class of plant E3 ubiquitin ligases. Immunoprecipitation-based methods are useful techniques for revealing interactions among Cullin-Ring Ligase (CRL) subunits or between CRLs and other proteins, as well as for detecting poly-ubiquitin modifications of the CRLs themselves. Here, we describe two immunoprecipitation (IP) procedures suitable for CRLs in Arabidopsis: (1) a procedure for IP analysis of CRL subunits and their interactors and a second procedure for in vivo ubiquitination analysis of the CRLs. Both protocols can be divided into two major steps: (1) preparation of cell extracts without disruption of protein interactions and (2) affinity purification of the protein complexes and subsequent detection. We provide a thorough description of all the steps, as well as advice on how to choose proper buffers for these analyses. We also suggest a series of negative controls that can be used to verify the specificity of the procedure.
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Affiliation(s)
- Federica Casagrande
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Giovanna Serino
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy.
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37
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Law HCH, Noe D, Woods NT. Interactome Profiling of DNA Damage Response (DDR) Mediators with Immunoprecipitation-Mass Spectrometry. Methods Mol Biol 2023; 2701:185-197. [PMID: 37574483 DOI: 10.1007/978-1-0716-3373-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Immunoprecipitation-mass spectrometry (IP-MS) is a versatile tool to probe for global protein-protein interactions (PPIs) in biological samples. Such interactions coordinate complex biological processes, such as the DNA damage response (DDR). Induction of DNA damage activates signaling networks where posttranslational modifications cause PPI that facilitate DNA repair and cell cycle coordination. Protein interactome profiling of DDR sensors, transducers, and effectors has the potential to identify novel DDR mechanisms that could advance our understanding and treatment of diseases associated with DDR defects, such as cancer. The protocol described here is a routine PPI analysis procedure that can be performed on samples stimulated with DNA damage. All processes and reagents are optimized for maximum sensitivity on the interactome and minimal contamination for the mass spectrometer.
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Affiliation(s)
- Henry C-H Law
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Dragana Noe
- Mass Spectrometry and Proteomics Core Facility, University of Nebraska Medical Center, Omaha, NE, USA
- Current address: Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Nicholas T Woods
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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38
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Chishti AA, Li Z, Liu B, Zhu WG. Assessing SIRT7 Activity In Vivo and In Vitro in Response to DNA Damage. Methods Mol Biol 2023; 2589:303-316. [PMID: 36255633 DOI: 10.1007/978-1-0716-2788-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The class III histone deacetylase (HDACs) also known as sirtuins (SIRTs 1-7) are ubiquitously expressed, but SIRT7 mainly resides as nucleolar protein. In this chapter a couple of methods are described that are used to detect modulation of SIRT7 in response to DNA damage. SIRT7 is localized in the nucleoli and binds to the chromatin after DNA damage. Therefore, a protocol was optimized by our lab for chromatin fractionation. By this method, the movement of SIRT7 can be detected from the soluble part (cytosol+nucleoplasm) to the solid part (chromatin) of the cell. Change of SIRT7 expression levels, in different cells or after different treatment, can be detected by isolating whole-cell lysate followed by Western blotting. For analyzing binding of SIRT7 to other substrates, we have also optimized manual immunoprecipitation assays by using 1% NP40 buffer. This protocol is very helpful to pull down SIRT7 and associated proteins by using a single buffer. SIRT7 is a deacetylase, and its deacetylation activity can be checked both inside the cell by in vivo deacetylation assay and outside the cell by in vitro deacetylation assays. Recently it was also discovered that SIRT7 has desuccinylase activity which can be detected by histone desuccinylation assay. This chapter provides the methodology of SIRT7 detection in the whole cell lysate, binding of SIRT7 to the chromatin and other proteins for performing deacetylation and desuccinylation activity.
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Affiliation(s)
- Arif Ali Chishti
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Zhenhai Li
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Baohua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
- National Engineering Research Center for Biotechnology (Shenzhen), Carson International Cancer Center, Medical Research Center, Shenzhen University Health Science Center, Shenzhen, China
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, China.
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China.
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Shenzhen University Health Science Center, Shenzhen, China.
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39
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Kuhn L, Vincent T, Hammann P, Zuber H. Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts. Methods Mol Biol 2023; 2426:243-265. [PMID: 36308692 DOI: 10.1007/978-1-0716-1967-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Immunoprecipitation mass spectrometry (IP-MS) is a popular method for the identification of protein-protein interactions. This approach is particularly powerful when information is collected without a priori knowledge and has been successively used as a first key step for the elucidation of many complex protein networks. IP-MS consists in the affinity purification of a protein of interest and of its interacting proteins followed by protein identification and quantification by mass spectrometry analysis. We developed an R package, named IPinquiry, dedicated to IP-MS analysis and based on the spectral count quantification method. The main purpose of this package is to provide a simple R pipeline with a limited number of processing steps to facilitate data exploration for biologists. This package allows to perform differential analysis of protein accumulation between two groups of IP experiments, to retrieve protein annotations, to export results, and to create different types of graphics. Here we describe the step-by-step procedure for an interactome analysis using IPinquiry from data loading to result export and plot production.
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Affiliation(s)
- Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Timothée Vincent
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade du CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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Bertgen L, Flohr T, Herrmann JM. Methods to Study the Biogenesis of Mitoribosomal Proteins in Yeast. Methods Mol Biol 2023; 2661:143-161. [PMID: 37166637 DOI: 10.1007/978-1-0716-3171-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The biogenesis of mitoribosomes is an intricate process that relies on the coordinated synthesis of nuclear-encoded mitoribosomal proteins (MRPs) in the cytosol, their translocation across mitochondrial membranes, the transcription of rRNA molecules in the matrix as well as the assembly of the roughly 80 different constituents of the mitoribosome. Numerous chaperones, translocases, processing peptidases, and assembly factors of the cytosol and in mitochondria support this complex reaction. The budding yeast Saccharomyces cerevisiae served as a powerful model organism to unravel the different steps by which MRPs are imported into mitochondria, fold into their native structures, and assemble into functional ribosomes.In this chapter, we provide established protocols to study these different processes experimentally. In particular, we describe methods to purify mitochondria from yeast cells, to import radiolabeled MRPs into isolated mitochondria, and to elucidate the assembly reaction of MRPs by immunoprecipitation. These protocols and the list of dos and don'ts will enable beginners and experienced scientists to study the import and assembly of MRPs.
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Affiliation(s)
- Lea Bertgen
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Tamara Flohr
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
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Noone J, Wallace RG, Rochfort KD. Immunoprecipitation: Variations, Considerations, and Applications. Methods Mol Biol 2023; 2699:271-303. [PMID: 37647004 DOI: 10.1007/978-1-0716-3362-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Immunoprecipitation (IP) refers to methods of affinity chromatography that enrich and/or purify a specific protein from a complex mixture using a specific antibody immobilized on a solid support. Several operations and processes that are dependent on the isolation, concentration, and modification of proteins have seen improvement in their selectivity and separation based on the integration of IP-specific reactions into their workflows. This relatively simple principle has contributed significantly to our understanding of proteins and their behaviors and has become increasingly fundamental to most protein characterization studies today. In this chapter, we review the basic principles of IP and the several factors that influence each stage, and subsequently the success, of an IP experiment. Moreover, variations in application of the IP principle are discussed, and the adaptability of the techniques based on such is highlighted in the provision of two IP workflows to purify a particular protein from an entire cellular proteosome. These workflows cover the preparation and fractionation of crude cellular lysate into individual subcellular fractions, through to both "batch" and "column"-based extractions of the target protein of interest. Protocols for determining the validity of the workflows, and the presence/abundance of the protein of interest, are also briefly described.
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Affiliation(s)
- John Noone
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- AdventHealth, Translational Research Institute, Orlando, Florida, United States of America
| | - Robert G Wallace
- School of Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
| | - Keith D Rochfort
- School of Nursing, Psychotherapy, and Community Health, Dublin City University, Glasnevin, Dublin, Ireland.
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Enyong EN, Gurley J, Sjoelung V, Elliott MH. Caveolin-1 in Müller Glia Exists as Heat-Resistant, High Molecular Weight Complexes. Adv Exp Med Biol 2023; 1415:249-256. [PMID: 37440041 DOI: 10.1007/978-3-031-27681-1_36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Caveolin-1 (Cav1), the core structural and scaffolding protein of caveolae membrane domains, is highly expressed in many retinal cells and is associated with ocular diseases. Cav1 regulates innate immune responses and is implicated in neuroinflammatory and neuroprotective signaling in the retina. We have shown that Cav1 expression in Müller glia accounts for over 70% of all retinal Cav1 expression. However, the proteins interacting with Cav1 in Müller glia are not established. Here, we show that immortalized MIO-M1 Müller glia, like endogenous Müller glia, highly express Cav1. Surprisingly, we found that Cav1 in MIO-M1 cells exists as heat-resistant, high molecular weight complexes that are stable after immunoprecipitation (IP). Mass spectrometric analysis of high molecular weight Cav1 complexes after Cav1 IP revealed an interactome network of intermediate filament, desmosomes, and actin-, and microtubule-based cytoskeleton. These results suggest Cav1 domains in Müller glia act as a scaffolding nexus for the cytoskeleton.
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Affiliation(s)
- Eric N Enyong
- Department of Physiology, Dean A. McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Ophthalmology, Dean A. McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jami Gurley
- Department of Physiology, Dean A. McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Ophthalmology, Dean A. McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Virginie Sjoelung
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael H Elliott
- Department of Physiology, Dean A. McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Ophthalmology, Dean A. McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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Pires G, Ueberheide B, Wisniewski T, Drummond E. Use of Affinity Purification-Mass Spectrometry to Identify Phosphorylated Tau Interactors in Alzheimer's Disease. Methods Mol Biol 2023; 2561:263-277. [PMID: 36399275 DOI: 10.1007/978-1-0716-2655-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Phosphorylated tau is the main protein present in neurofibrillary tangles, the presence of which is a key neuropathological hallmark of Alzheimer's disease (AD). The toxic effects of phosphorylated tau are likely mediated by interacting proteins; however, methods to identify these interacting proteins comprehensively in human brain tissue are limited. Here, we describe a method that enables the efficient identification of hundreds of proteins that interact with phosphorylated tau (pTau), using affinity purification-mass spectrometry (AP-MS) on human, fresh-frozen brain tissue from donors with AD. Tissue is homogenized using a gentle technique that preserves protein-protein interactions, and co-immunoprecipitation of pTau and its interacting proteins is performed using the PHF1 antibody. The resulting protein interactors are then identified using label-free quantitative liquid chromatography-mass spectrometry (LC-MS)/MS. The Significance Analysis of INTeractome (SAINT) algorithm is used to determine which proteins significantly interact with pTau. This approach enables the detection of an abundance of all 6 isoforms of tau, 23 phosphorylated residues on tau, and 125 significant pTau protein interactors, in human AD brain tissue.
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Affiliation(s)
- Geoffrey Pires
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, USA
- Alzheimer's and Prion Diseases Team, Paris Brain Institute, CNRS, UMR 7225, INSERM 1127, Sorbonne University UM75, Paris, France
| | - Beatrix Ueberheide
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, USA
- Departments of Pathology and Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Eleanor Drummond
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, USA.
- Brain & Mind Center and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
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Dauben H, Matic I. Immunoprecipitation Using Mono-ADP-Ribosylation-Specific Antibodies. Methods Mol Biol 2023; 2609:135-46. [PMID: 36515834 DOI: 10.1007/978-1-0716-2891-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Immunoprecipitation is an essential methodology for enriching and purifying targeted proteins and peptides for in-depth analysis by any number of further techniques, from Western blotting to mass spectrometry (MS). Historically, the posttranslational modification ADP-ribosylation (ADPr) has been studied mainly in its polymerized form (poly-ADPr), but recent studies support the abundance and physiological relevance of mono-ADPr. Here, we describe several approaches to enrich mono-ADP-ribosylated proteins and peptides using mono-ADPr-specific antibodies, which can be tailored to a desired target and mode of downstream analysis.
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Fortunato D, Giannoukakos S, Giménez-Capitán A, Hackenberg M, Molina-Vila MA, Zarovni N. Selective isolation of extracellular vesicles from minimally processed human plasma as a translational strategy for liquid biopsies. Biomark Res 2022; 10:57. [PMID: 35933395 PMCID: PMC9357340 DOI: 10.1186/s40364-022-00404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Background Intercellular communication is mediated by extracellular vesicles (EVs), as they enclose selectively packaged biomolecules that can be horizontally transferred from donor to recipient cells. Because all cells constantly generate and recycle EVs, they provide accurate timed snapshots of individual pathophysiological status. Since blood plasma circulates through the whole body, it is often the biofluid of choice for biomarker detection in EVs. Blood collection is easy and minimally invasive, yet reproducible procedures to obtain pure EV samples from circulating biofluids are still lacking. Here, we addressed central aspects of EV immunoaffinity isolation from simple and complex matrices, such as plasma. Methods Cell-generated EV spike-in models were isolated and purified by size-exclusion chromatography, stained with cellular dyes and characterized by nano flow cytometry. Fluorescently-labelled spike-in EVs emerged as reliable, high-throughput and easily measurable readouts, which were employed to optimize our EV immunoprecipitation strategy and evaluate its performance. Plasma-derived EVs were captured and detected using this straightforward protocol, sequentially combining isolation and staining of specific surface markers, such as CD9 or CD41. Multiplexed digital transcript detection data was generated using the Nanostring nCounter platform and evaluated through a dedicated bioinformatics pipeline. Results Beads with covalently-conjugated antibodies on their surface outperformed streptavidin-conjugated beads, coated with biotinylated antibodies, in EV immunoprecipitation. Fluorescent EV spike recovery evidenced that target EV subpopulations can be efficiently retrieved from plasma, and that their enrichment is dependent not only on complex matrix composition, but also on the EV surface phenotype. Finally, mRNA profiling experiments proved that distinct EV subpopulations can be captured by directly targeting different surface markers. Furthermore, EVs isolated with anti-CD61 beads enclosed mRNA expression patterns that might be associated to early-stage lung cancer, in contrast with EVs captured through CD9, CD63 or CD81. The differential clinical value carried within each distinct EV subset highlights the advantages of selective isolation. Conclusions This EV isolation protocol facilitated the extraction of clinically useful information from plasma. Compatible with common downstream analytics, it is a readily implementable research tool, tailored to provide a truly translational solution in routine clinical workflows, fostering the inclusion of EVs in novel liquid biopsy settings. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-022-00404-1.
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Garg P, Semmler S, Baudouin C, Velde CV, Plotkin SS. Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6. J Mol Biol 2022; 434:167697. [PMID: 35753527 DOI: 10.1016/j.jmb.2022.167697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/14/2022] [Accepted: 06/18/2022] [Indexed: 10/17/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease primarily impacting motor neurons. Mutations in superoxide dismutase 1 (SOD1) are the second most common cause of familial ALS. Several of these mutations lead to misfolding or toxic gain of function in the SOD1 protein. Recently, we reported that misfolded SOD1 interacts with TNF receptor-associated factor 6 (TRAF6) in the SOD1G93A rat model of ALS. Further, we showed in cultured cells that several mutant SOD1 proteins, but not wildtype SOD1 protein, interact with TRAF6 via the MATH domain. Here, we sought to uncover the structural details of this interaction through molecular dynamics (MD) simulations of a dimeric model system, coarse grained using the AWSEM force field. We used direct MD simulations to identify buried residues, and predict binding poses by clustering frames from the trajectories. Metadynamics simulations were also used to deduce preferred binding regions on the protein surfaces from the potential of the mean force in orientation space. Well-folded SOD1 was found to bind TRAF6 via co-option of its native homodimer interface. However, if loops IV and VII of SOD1 were disordered, as typically occurs in the absence of stabilizing Zn2+ ion binding, these disordered loops now participated in novel interactions with TRAF6. On TRAF6, multiple interaction hot-spots were distributed around the equatorial region of the MATH domain beta barrel. Expression of TRAF6 variants with mutations in this region in cultured cells demonstrated that TRAF6T475 facilitates interaction with different SOD1 mutants. These findings contribute to our understanding of the disease mechanism and uncover potential targets for the development of therapeutics.
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Affiliation(s)
- Pranav Garg
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Sabrina Semmler
- Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec H3A 2B4, Canada; Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada
| | - Charlotte Baudouin
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada; Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Christine Vande Velde
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada; Department of Neurosciences, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada; Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
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Xu W, Zheng J, Wang X, Zhou B, Chen H, Li G, Yan F. tRF-Val-CAC-016 modulates the transduction of CACNA1d-mediated MAPK signaling pathways to suppress the proliferation of gastric carcinoma. Cell Commun Signal 2022; 20:68. [PMID: 35590368 PMCID: PMC9118711 DOI: 10.1186/s12964-022-00857-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 03/04/2022] [Indexed: 11/25/2022] Open
Abstract
Background As a new kind of non-coding RNAs (ncRNAs), tRNA derivatives play an important role in gastric carcinoma (GC). Nevertheless, the underlying mechanism tRNA derivatives were involved in was rarely illustrated. Methods We screened out the tRNA derivative, tRF-Val-CAC-016, based on the tsRNA sequencing and demonstrated the effect tRF-Val-CAC-016 exerted on GC proliferation in vitro and in vivo. We applied Dual-luciferase reporter assay, RIP assay, and bioinformatic analysis to discover the downstream target of tRF-Val-CAC-016. Then CACNA1d was selected, and the oncogenic characteristics were verified. Subsequently, we detected the possible regulation of the canonical MAPK signaling pathway to further explore the downstream mechanism of tRF-Val-CAC-016. Results As a result, we found that tRF-Val-CAC-016 was low-expressed in GC, and upregulation of tRF-Val-CAC-016 could significantly suppress the proliferation of GC cell lines. Meanwhile, tRF-Val-CAC-016 regulated the canonical MAPK signaling pathway by targeting CACNA1d. Conclusions tRF-Val-CAC-016 modulates the transduction of CACNA1d-mediated MAPK signaling pathways to suppress the proliferation of gastric carcinoma. This study discussed the function and mechanism of tRF-Val-CAC-016 in GC for the first time. The pioneering work has contributed to our present understanding of tRNA derivative, which might provide an alternative mean for the targeted therapy of GC. Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00857-9.
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Affiliation(s)
- Weiguo Xu
- Department of General Surgery, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Junyu Zheng
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China
| | - Xiao Wang
- Department of Radiology, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Bin Zhou
- Department of Gastric Surgery, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China
| | - Huanqiu Chen
- Department of Gastric Surgery, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China.
| | - Gang Li
- Department of Gastric Surgery, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China.
| | - Feng Yan
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Institute of Cancer Research, Baiziting No. 42, Nanjing, 210009, Jiangsu, China.
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Yadav VK, Awasthi P, Behl R, Kumar A. HSc70 interactome reveal major role of macroautophagy and minor role of chaperone mediated autophagy in K-Ras G12V cell proliferation and survival. J Proteomics 2022;:104614. [PMID: 35595057 DOI: 10.1016/j.jprot.2022.104614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/28/2022] [Accepted: 05/08/2022] [Indexed: 11/23/2022]
Abstract
Constitutively active K-Ras oncogene mutation at G12V changes the proteome of cells and activates macroautophagy for cell advantage. Inhibition of macroautophagy impairs K-Ras mediated tumor progression to a limited extent with increase of spontaneous tumors due to poorly understood mechanisms. Here, we show that inhibition of macroautophagy in K-Ras G12V mouse embryonic fibroblasts (MEFs) hyper activates chaperon mediated autophagy (CMA). Quantitative identification of CMA substrates through co-immunoprecipitation of CMA component heat shock cognate 70 (Hsc70) demonstrates a shift of proteins from macroautophagy to CMA mediated degradation. However, macroautophagy impairment show significant inhibition on proliferation and CMA hyper activation provides a basal support to macroautophagy-inhibited MEFs for survival. On the other hand, K-Ras G12V MEFs impaired of CMA reduces number of Hsc70 clients but activated macroautophagy significantly compensated CMA loss. Nonetheless, co-inhibition of CMA and macroautophagy had a synergistic detrimental effect on both proliferation and survival of MEFs expressing K-Ras G12V mutant. Our results point to K-Ras G12V MEFs dependency on macroautophagy and CMA partly compensates its loss for survival but not hyper-proliferation; implicating that targeting both macroautophagy and CMA as a promising therapeutic target in G12V mutation associated K-Ras cancers. SIGNIFICANCE: The present study provides a framework of Hsc70 interacting proteins, which differentially interact with Hsc70 in response to autophagy alterations. The role of proteins accumulation and induced proteo-toxicity could be underlying factor in macroautophagy and CMA co-inhibited K-Ras G12V MEFs phenotype. Our study provides rational for adaptive mechanisms in K-Ras tumors inhibited with different autophagy pathways and also supports targeting both macroautophagy and CMA simultaneously as therapeutic target. At the same time current study will help in characterizing the underlying cellular processes that may play a role in escaping tutor suppressor role CMA and macroautophagy in cancers harboring K-Ras G12V mutation that may be further utilized to identify molecular targets for K-Ras-driven cancers.
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Kitchen P, Gaston K, Jayaraman PS. Transcription Factor Chromatin Immunoprecipitation in Endothelial Cells. Methods Mol Biol 2022; 2441:257-275. [PMID: 35099743 DOI: 10.1007/978-1-0716-2059-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions between DNA and proteins are crucial for the regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful technique that allows the study of specific protein-DNA interactions in cultured cells and fresh or fixed tissue. Chromatin is isolated and sheared, and antibodies against the protein(s) of interest are used to isolate specific protein-DNA complexes. Subsequent analysis by real-time polymerase chain reaction (qPCR) or next-generation sequencing (NGS) allows identification and quantification of the co-purified DNA fragments, and NGS also gives insight into the genomic binding sites of a protein. Here we describe a cross-linking ChIP (X-ChIP) protocol, based around the example of a myc-tagged Proline-Rich Homeodomain (PRH) protein expressed in human umbilical vein endothelial cells. We also describe how to analyse specific known or suspected binding sites using quantitative PCR as well as how to analyse genome-wide binding from ChIP sequencing data.
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Affiliation(s)
- Philip Kitchen
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Kevin Gaston
- Biodiscovery Institute and Division of Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Padma-Sheela Jayaraman
- Biodiscovery Institute and Division of Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK.
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Abstract
Immunoprecipitation of protein complexes, also known as co-immunoprecipitation (Co-IP), is a powerful technique to analyze protein-protein interactions. Commercial availability of Dynabeads® Protein A magnetic beads provides a fast, convenient, and efficient method for protein interaction studies by Co-IP followed by immunoblotting (Co-IP-blotting). Recently, the Co-IP-blotting technique helped us to investigate complicated protein interactions/networks involving nuclear protein 1 (Nupr1), a recently discovered regulator of apoptosis in human cartilage cells. The methods and protocols for Co-IP-blotting are reported here in detail.
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Affiliation(s)
- Li Tan
- Section of Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Raghunatha R Yammani
- Section of Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
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