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Herianto S, Subramani B, Chen BR, Chen CS. Recent advances in liposome development for studying protein-lipid interactions. Crit Rev Biotechnol 2024; 44:1-14. [PMID: 36170980 DOI: 10.1080/07388551.2022.2111294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/12/2022] [Accepted: 05/29/2022] [Indexed: 11/03/2022]
Abstract
Protein-lipid interactions are crucial for various cellular biological processes like intracellular signaling, membrane transport, and cytoskeletal dynamics. Therefore, studying these interactions is essential to understand and unravel their specific functions. Nevertheless, the interacting proteins of many lipids are poorly understood and still require systematic study. Liposomes are the most well-known and familiar biomimetic systems used to study protein-lipid interactions. Although liposomes have been widely used for studying protein-lipid interactions in classical methods such as the co-flotation assay (CFA), co-sedimentation assay (CSA), and flow cytometric assay (FCA), an overview of their current applications and developments in high-throughput methods is not yet available. Here, we summarize the liposome development in low and high-throughput methods to study protein-lipid interactions. Besides, a constructive comment for each platform is presented to stimulate the advancement of these technologies in the future.
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Affiliation(s)
- Samuel Herianto
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Chemistry (Chemical Biology Division), College of Science, National Taiwan University, Taipei, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Boopathi Subramani
- Institute of Food Science and Technology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bo-Ruei Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Caligaris M, Sampaio-Marques B, Hatakeyama R, Pillet B, Ludovico P, De Virgilio C, Winderickx J, Nicastro R. The Yeast Protein Kinase Sch9 Functions as a Central Nutrient-Responsive Hub That Calibrates Metabolic and Stress-Related Responses. J Fungi (Basel) 2023; 9:787. [PMID: 37623558 PMCID: PMC10455444 DOI: 10.3390/jof9080787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Yeast cells are equipped with different nutrient signaling pathways that enable them to sense the availability of various nutrients and adjust metabolism and growth accordingly. These pathways are part of an intricate network since most of them are cross-regulated and subject to feedback regulation at different levels. In yeast, a central role is played by Sch9, a protein kinase that functions as a proximal effector of the conserved growth-regulatory TORC1 complex to mediate information on the availability of free amino acids. However, recent studies established that Sch9 is more than a TORC1-effector as its activity is tuned by several other kinases. This allows Sch9 to function as an integrator that aligns different input signals to achieve accuracy in metabolic responses and stress-related molecular adaptations. In this review, we highlight the latest findings on the structure and regulation of Sch9, as well as its role as a nutrient-responsive hub that impacts on growth and longevity of yeast cells. Given that most key players impinging on Sch9 are well-conserved, we also discuss how studies on Sch9 can be instrumental to further elucidate mechanisms underpinning healthy aging in mammalians.
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Affiliation(s)
- Marco Caligaris
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (B.S.-M.); (P.L.)
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Riko Hatakeyama
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Benjamin Pillet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (B.S.-M.); (P.L.)
- ICVS/3B’s-PT Government Associate Laboratory, 4806-909 Guimarães, Portugal
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, B-3001 Heverlee, Belgium;
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; (M.C.); (B.P.); (C.D.V.)
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Herianto S, Chien PJ, Ho JAA, Tu HL. Liposome-based artificial cells: From gene expression to reconstitution of cellular functions and phenotypes. BIOMATERIALS ADVANCES 2022; 142:213156. [PMID: 36302330 DOI: 10.1016/j.bioadv.2022.213156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Bottom-up approaches in creating artificial cells that can mimic natural cells have significant implications for both basic research and translational application. Among various artificial cell models, liposome is one of the most sophisticated systems. By encapsulating proteins and associated biomolecules, they can functionally reconstitute foundational features of biological cells, such as the ability to divide, communicate, and undergo shape deformation. Yet constructing liposome artificial cells from the genetic level, which is central to generate self-sustained systems remains highly challenging. Indeed, many studies have successfully established the expression of gene-coded proteins inside liposomes. Further, recent endeavors to build a direct integration of gene-expressed proteins for reconstituting molecular functions and phenotypes in liposomes have also significantly increased. Thus, this review presents the development of liposome-based artificial cells to demonstrate the process of gene-expressed proteins and their reconstitution to perform desired molecular and cell-like functions. The molecular and cellular phenotypes discussed here include the self-production of membrane phospholipids, division, shape deformation, self-DNA/RNA replication, fusion, and intercellular communication. Together, this review gives a comprehensive overview of gene-expressing liposomes that can stimulate further research of this technology and achieve artificial cells with superior properties in the future.
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Affiliation(s)
- Samuel Herianto
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Chien
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ja-An Annie Ho
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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Rathod J, Yen HC, Liang B, Tseng YY, Chen CS, Wu WS. YPIBP: A repository for phosphoinositide-binding proteins in yeast. Comput Struct Biotechnol J 2021; 19:3692-3707. [PMID: 34285772 PMCID: PMC8261538 DOI: 10.1016/j.csbj.2021.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.
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Key Words
- ANTH, AP180 N-terminal Homology
- BAR, Bin-Amphiphysin-Rvs
- CAFA, Critical Assessment of Functional Annotation
- CRAL-TRIO, cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor
- Cvt, Cytoplasm-to-vacuole targeting
- ENTH, Epsin N-terminal Homology
- FDR, False Discovery Rate
- FYVE, Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1
- GO, Gene Ontology
- ITC, Isothermal Titration Calorimetry
- LBD, Lipid-Binding Domain
- LMPD, LIPID MAPS Proteome Database
- LMSD, LIPID MAPS Structure Database
- LRD, Lipid-Related Domain
- Lipid-binding domain
- OMIM, Online Mendelian Inheritance in Man
- OSBP, Oxysterol-Binding Protein
- PH, Pleckstrin Homology
- PI(3,4)P2, phosphatidylinositol-3,4-bisphosphate
- PI(3,4,5)P3, phosphatidylinositol-3,4,5-trisphosphate
- PI(3,5)P2, phosphatidylinositol-3,5-bisphosphate
- PI(4,5)P2, phosphatidylinositol-4,5-bisphosphate
- PI-binding protein
- PI3P, phosphatidylinositol-3-phosphate
- PI4P, phosphatidylinositol-4-phosphate
- PI5P, phosphatidylinositol-5-phosphate
- PIs, Phosphoinositides
- PMID, PubMed ID
- PX, Phox Homology
- Phosphatidylinositol (PtdIns)
- Phosphoinositides (PIs)
- PtdIns, Phosphatidylinositol
- QCM, Quartz Crystal Microbalance
- S. cerevisiae
- SNX, Sorting Nexin
- SPR, Surface Plasmon Resonance
- YPIBP, Yeast Phosphoinositide-Binding Proteins
- Yeast
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Affiliation(s)
- Jagat Rathod
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Han-Chen Yen
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Biqing Liang
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
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Systematic Identification of Protein Targets of Sub5 Using Saccharomyces cerevisiae Proteome Microarrays. Int J Mol Sci 2021; 22:ijms22020760. [PMID: 33451135 PMCID: PMC7828587 DOI: 10.3390/ijms22020760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial peptides (AMPs) are intensively studied in terms of alternative drugs. Sub5 is a synthetic 12-mer AMP with substitutions of five amino acids of bactenecin 2A (Bac2A), a linear-ized bactenecin variant of bovine. Sub5 is highly effective against fungi with an ability to trans-locate cell membrane, but its targets are unknown. Systematic analysis of Sub5 targets will facil-itate our understanding on its mechanism of action. In this study, we used high-throughput Saccharomyces cerevisiae proteome microarrays to explore the potential protein targets of Sub5. The screening results showed 128 potential protein targets of Sub5. Bioinformatics analysis of protein targets of Sub5 revealed significant gene ontology (GO) enrichment in actin related pro-cess of “actin filament-based process”, “actin filament organization”, “actin cortical patch or-ganization”, regulation of “actin filament bundle assembly”. Moreover, the other enriched cat-egories in GO enrichment mostly contained actin associate proteins. In total, 11 actin-associated proteins were identified in the protein targets of Sub5. Protein family (PFAM) enrichment anal-ysis shows protein domain enriched in actin binding, i.e., “Cytoskeletal-regulatory complex EF hand (helix E-loop-helix F motif)”. Being consistent with GO analysis, Search Tool for the Re-trieval of Interacting Genes/Proteins (STRING) analysis of the protein targets of Sub5 showed ac-tin network with involvement of 15 protein targets. Along with actin-network, STRING analysis showed protein–protein interaction network in ribonucleoprotein, transcription and translation, chromosome, histone, and ubiquitin related, DNA repair, and chaperone. Multiple Expression motifs for Motif Elicitation (MEME) suite provided a consensus binding motif of [ED][ED]EEE[ED][ED][ED][ED][ED], in total of 75 protein targets of Sub5. This motif was present in 9 out of 15 actin-related proteins identified among protein targets of Sub5.
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Frankovsky J, Vozáriková V, Nosek J, Tomáška Ľ. Mitochondrial protein phosphorylation in yeast revisited. Mitochondrion 2021; 57:148-162. [PMID: 33412333 DOI: 10.1016/j.mito.2020.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022]
Abstract
Protein phosphorylation is one of the best-known post-translational modifications occurring in all domains of life. In eukaryotes, protein phosphorylation affects all cellular compartments including mitochondria. High-throughput techniques of mass spectrometry combined with cell fractionation and biochemical methods yielded thousands of phospho-sites on hundreds of mitochondrial proteins. We have compiled the information on mitochondrial protein kinases and phosphatases and their substrates in Saccharomyces cerevisiae and provide the current state-of-the-art overview of mitochondrial protein phosphorylation in this model eukaryote. Using several examples, we describe emerging features of the yeast mitochondrial phosphoproteome and present challenges lying ahead in this exciting field.
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Affiliation(s)
- Jan Frankovsky
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
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7
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Herianto S, Rathod J, Shah P, Chen YZ, Wu WS, Liang B, Chen CS. Systematic Analysis of Phosphatidylinositol-5-phosphate-Interacting Proteins Using Yeast Proteome Microarrays. Anal Chem 2020; 93:868-877. [PMID: 33302626 DOI: 10.1021/acs.analchem.0c03463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We used yeast proteome microarrays (∼5800 purified proteins) to conduct a high-throughput and systematic screening of PI5P-interacting proteins with PI5P-tagged fluorescent liposomal nanovesicles. Lissamine rhodamine B-dipalmitoyl phosphatidylethanol was incorporated into the liposome bilayer to provide the nanovesicles with fluorescence without any encapsulants, which not only made the liposome fabrication much easier without the need for purification but also improved the chip-probing quality. A special chip assay was washed very gently without the traditional spin-dry step. Forty-five PI5P-interacting proteins were identified in triplicate with this special chip assay. Subsequently, we used flow cytometry to validate these interactions, and a total of 41 PI5P-interacting proteins were confirmed. Enrichment analysis revealed that these proteins have significant functions associated with ribosome biogenesis, rRNA processing, ribosome binding, GTP binding, and hydrolase activity. Their component enrichment is located in the nucleolus. The InterPro domain analysis indicated that PI5P-interacting proteins are enriched in the P-loop containing nucleoside triphosphate hydrolases domain (P-loop). Additionally, using the MEME program, we identified a consensus motif (IVGPAGTGKSTLF) that contains the Walker A sequence, a well-known nucleotide-binding motif. Furthermore, using a quartz crystal microbalance, both the consensus motif and Walker A motif showed strong affinities to PI5P-containing liposomes but not to PI5P-deprived liposomes or PI-containing liposomes. Additionally, the glycine (G6) and lysine (K7) residues of the Walker A motif (-GPAGTG6K7S-) were found to be critical to the PI5P-binding ability. This study not only identified an additional set of PI5P-interacting proteins but also revealed the strong PI5P-binding affinity (Kd = 1.81 × 10-7 M) of the Walker A motif beyond the motif's nucleotide-binding characteristic.
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Affiliation(s)
- Samuel Herianto
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Jagat Rathod
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Pramod Shah
- Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Jhongli 300, Taiwan
| | - You-Zuo Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Biqing Liang
- Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
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8
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Lu KY, Pasaje CFA, Srivastava T, Loiselle DR, Niles JC, Derbyshire E. Phosphatidylinositol 3-phosphate and Hsp70 protect Plasmodium falciparum from heat-induced cell death. eLife 2020; 9:e56773. [PMID: 32975513 PMCID: PMC7518890 DOI: 10.7554/elife.56773] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022] Open
Abstract
Phosphatidylinositol 3-phosphate (PI(3)P) levels in Plasmodium falciparum correlate with tolerance to cellular stresses caused by artemisinin and environmental factors. However, PI(3)P function during the Plasmodium stress response was unknown. Here, we used PI3K inhibitors and antimalarial agents to examine the importance of PI(3)P under thermal conditions recapitulating malarial fever. Live cell microscopy using chemical and genetic reporters revealed that PI(3)P stabilizes the digestive vacuole (DV) under heat stress. We demonstrate that heat-induced DV destabilization in PI(3)P-deficient P. falciparum precedes cell death and is reversible after withdrawal of the stress condition and the PI3K inhibitor. A chemoproteomic approach identified PfHsp70-1 as a PI(3)P-binding protein. An Hsp70 inhibitor and knockdown of PfHsp70-1 phenocopy PI(3)P-deficient parasites under heat shock. Furthermore, PfHsp70-1 downregulation hypersensitizes parasites to heat shock and PI3K inhibitors. Our findings underscore a mechanistic link between PI(3)P and PfHsp70-1 and present a novel PI(3)P function in DV stabilization during heat stress.
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Affiliation(s)
- Kuan-Yi Lu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke UniversityDurhamUnited States
- Department of Chemistry, Duke UniversityDurhamUnited States
| | | | | | - David R Loiselle
- Department of Pharmacology and Cancer Biology, School of Medicine, Duke UniversityDurhamUnited States
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Emily Derbyshire
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke UniversityDurhamUnited States
- Department of Chemistry, Duke UniversityDurhamUnited States
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Shah P, Wu WS, Chen CS. Systematical Analysis of the Protein Targets of Lactoferricin B and Histatin-5 Using Yeast Proteome Microarrays. Int J Mol Sci 2019; 20:ijms20174218. [PMID: 31466342 PMCID: PMC6747642 DOI: 10.3390/ijms20174218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial peptides (AMPs) have potential antifungal activities; however, their intracellular protein targets are poorly reported. Proteome microarray is an effective tool with high-throughput and rapid platform that systematically identifies the protein targets. In this study, we have used yeast proteome microarrays for systematical identification of the yeast protein targets of Lactoferricin B (Lfcin B) and Histatin-5. A total of 140 and 137 protein targets were identified from the triplicate yeast proteome microarray assays for Lfcin B and Histatin-5, respectively. The Gene Ontology (GO) enrichment analysis showed that Lfcin B targeted more enrichment categories than Histatin-5 did in all GO biological processes, molecular functions, and cellular components. This might be one of the reasons that Lfcin B has a lower minimum inhibitory concentration (MIC) than Histatin-5. Moreover, pairwise essential proteins that have lethal effects on yeast were analyzed through synthetic lethality. A total of 11 synthetic lethal pairs were identified within the protein targets of Lfcin B. However, only three synthetic lethal pairs were identified within the protein targets of Histatin-5. The higher number of synthetic lethal pairs identified within the protein targets of Lfcin B might also be the reason for Lfcin B to have lower MIC than Histatin-5. Furthermore, two synthetic lethal pairs were identified between the unique protein targets of Lfcin B and Histatin-5. Both the identified synthetic lethal pairs proteins are part of the Spt-Ada-Gcn5 acetyltransferase (SAGA) protein complex that regulates gene expression via histone modification. Identification of synthetic lethal pairs between Lfcin B and Histatin-5 and their involvement in the same protein complex indicated synergistic combination between Lfcin B and Histatin-5. This hypothesis was experimentally confirmed by growth inhibition assay.
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Affiliation(s)
- Pramod Shah
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
- Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan City 701, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan.
- Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan.
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan City 701, Taiwan.
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10
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Yang D, Liu D, Deng H, Zhang J, Qin M, Yuan L, Zou X, Shao B, Li H, Dai W, Zhang H, Wang X, He B, Tang X, Zhang Q. Transferrin Functionization Elevates Transcytosis of Nanogranules across Epithelium by Triggering Polarity-Associated Transport Flow and Positive Cellular Feedback Loop. ACS NANO 2019; 13:5058-5076. [PMID: 31034211 DOI: 10.1021/acsnano.8b07231] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Overcoming the epithelial barriers to enhance drug transport is a focused topic for gastrointestinal, intratracheal, intranasal, vaginal, and intrauterine delivery. Nanomedicines with targeting functionization promote such a process owing to specific ligand-receptor interaction. However, compared to the cell uptake of targeting nanotherapies, currently few studies concentrate on their transcytosis including endocytosis for "in" and exocytosis for "out". In fact, the cellular regulatory mechanism for these pathways as well as the principle of ligand's effect on the transcytosis are almost ignored. Here, we fabricated transferrin (Tf) functionalized nanogranules (Tf-NG) as the nanomedicine model and confirmed the difference in polar distributions of Tf receptors (TfRs) between two epithelium models (bipolarity for Caco-2 and unipolarity for MDCK cells). Compared to the nonspecific reference, Tf-conjugation boosted the endocytosis by different pathways in two cell models and transformed the intracellular route of Tf-NG in both cells differently, affecting exocytosis, recycling, and degradation but not the secretion pathway. Only bipolar cells could establish a complete transport flow from "in" to "out", leading to the enhanced transcytosis of Tf-NG. Importantly, epithelia could make responses to Tf-NG transcytosis. Based on the quantitative proteomics, the intracellular trafficking of Tf-NG altered the protein expression profiles, in which the endocytosis- and transcytosis-related proteins were specifically upregulated. Particularly, only bipolar cells could positively feed back to such trafficking via accelerating the subsequent Tf-NG transcytosis. Here, all the cell transport of Tf-NG was polarity associated. In summary, Tf modification elevated the transcytosis of Tf-NG across the epithelium by triggering the polarity-associated transport flow and positive cell feedback loop. These findings provided an insight into the targeting nanodelivery for efficient transport through epithelial barriers.
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Affiliation(s)
- Dan Yang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- School of Pharmacy , Shenyang Pharmaceutical University , Shenyang 110016 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Dechun Liu
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Hailiang Deng
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Jian Zhang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Mengmeng Qin
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Lan Yuan
- Centre of Medical and Health Analysis , Peking University , Beijing 100191 , China
| | - Xiajuan Zou
- Centre of Medical and Health Analysis , Peking University , Beijing 100191 , China
| | - Bin Shao
- Department of Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) , Peking University Cancer Hospital and Institute , Beijing 100142 , China
| | - Huiping Li
- Department of Medical Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) , Peking University Cancer Hospital and Institute , Beijing 100142 , China
| | - Wenbing Dai
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Hua Zhang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Xueqing Wang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Bing He
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
| | - Xing Tang
- School of Pharmacy , Shenyang Pharmaceutical University , Shenyang 110016 , China
| | - Qiang Zhang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
- School of Pharmacy , Shenyang Pharmaceutical University , Shenyang 110016 , China
- State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing 100191 , China
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11
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Glantz ST, Berlew EE, Chow BY. Synthetic cell-like membrane interfaces for probing dynamic protein-lipid interactions. Methods Enzymol 2019; 622:249-270. [PMID: 31155055 DOI: 10.1016/bs.mie.2019.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The ability to rapidly screen interactions between proteins and membrane-like interfaces would aid in establishing the structure-function of protein-lipid interactions, provide a platform for engineering lipid-interacting protein tools, and potentially inform the signaling mechanisms and dynamics of membrane-associated proteins. Here, we describe the preparation and application of water-in-oil (w/o) emulsions with lipid-stabilized droplet interfaces that emulate the plasma membrane inner leaflet with tunable composition. Fluorescently labeled proteins are easily visualized in these synthetic cell-like droplets on an automated inverted fluorescence microscope, thus allowing for both rapid screening of relative binding and spatiotemporally resolved analyses of for example, protein-interface association and dissociation dynamics and competitive interactions, using commonplace instrumentation. We provide protocols for droplet formation, automated imaging assays and analysis, and the production of the positive control protein BcLOV4, a natural photoreceptor with a directly light-regulated interaction with anionic membrane phospholipids that is useful for optogenetic membrane recruitment.
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Affiliation(s)
- Spencer T Glantz
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Erin E Berlew
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States.
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12
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Herianto S, Chen CS, Zhu H. Protein Microarrays and Liposome: A Method for Studying Lipid-Protein Interactions. Methods Mol Biol 2019; 2003:191-199. [PMID: 31218620 DOI: 10.1007/978-1-4939-9512-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Interactions between specific lipids and proteins can provide important information regarding the functions of proteins and lipids. One of the novel and powerful methods to identify lipid-protein interactions is using protein microarrays and liposomes. Liposomes are spherical vesicles that are surrounded by phospholipid bilayers in which the lipid of interest can be incorporated. Thus, liposomes can be used to detect lipid-protein interactions and to analyze interactions between thousands of proteins and a small number of lipids with a single experiment. This chapter presents the methods and procedures for using protein microarray assays and liposome fabrication to analyze protein-lipid interactions. Up-to-date research reports are also reviewed briefly.
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Affiliation(s)
- Samuel Herianto
- High Throughput Biosensing Laboratory, Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Chien-Sheng Chen
- High Throughput Biosensing Laboratory, Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan City, Taiwan.
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences/High-Throughput Biology Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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13
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Abstract
The utilization of light energy to power organic-chemical transformations is a fundamental strategy of the terrestrial energy cycle. Inspired by the elegance of natural photosynthesis, much interdisciplinary research effort has been devoted to the construction of simplified cell mimics based on artificial vesicles to provide a novel tool for biocatalytic cascade reactions with energy-demanding steps. By inserting natural or even artificial photosynthetic systems into liposomes or polymersomes, the light-driven proton translocation and the resulting formation of electrochemical gradients have become possible. This is the basis for the conversion of photonic into chemical energy in form of energy-rich molecules such as adenosine triphosphate (ATP), which can be further utilized by energy-dependent biocatalytic reactions, e.g. carbon fixation. This review compares liposomes and polymersomes as artificial compartments and summarizes the types of light-driven proton pumps that have been employed in artificial photosynthesis so far. We give an overview over the methods affecting the orientation of the photosystems within the membranes to ensure a unidirectional transport of molecules and highlight recent examples of light-driven biocatalysis in artificial vesicles. Finally, we summarize the current achievements and discuss the next steps needed for the transition of this technology from the proof-of-concept status to preparative applications.
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14
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Feng Y, Chen CS, Ho J, Pearce D, Hu S, Wang B, Desai P, Kim KS, Zhu H. High-Throughput Chip Assay for Investigating Escherichia coli Interaction with the Blood-Brain Barrier Using Microbial and Human Proteome Microarrays (Dual-Microarray Technology). Anal Chem 2018; 90:10958-10966. [PMID: 30106562 DOI: 10.1021/acs.analchem.8b02513] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacterial meningitis in neonates and infants is an acute lethal disease and occurs in response to microbial exploitation of the blood-brain barrier (BBB), resulting in the intracranial inflammation. Several pathogens, such as Escherichia coli ( E. coli), can cause this devastating disease; however, the underlying molecular mechanisms by which these pathogens exploit the BBB remain incompletely understood. To identify important players on both the pathogen and host sides that govern the E. coli-BBB cell interactions, we took advantage of the E. coli and human proteome microarrays (i.e., HuProt) as an unbiased, proteome-wide tool for identification of important players on both sides. Using the E. coli proteome microarrays, we developed a unique high throughput chip-based cell probing assay to probe with fluorescent live human brain microvascular endothelial cells (HBMEC, which constitute the BBB). We identified several transmembrane proteins, which effectively bound to live HBMEC. We focused on YojI protein for further study. By probing the HuProt arrays with YojI, interferon-alpha receptor (IFNAR2) was identified as one of its binding proteins. The importance of YojI and IFNAR2 involved in E. coli-HBMEC interactions was characterized using the YojI knockout bacteria and IFNAR2-knock down HBMEC and further confirmed by E. coli binding assay in HBMEC. This study represents a new paradigm (dual-microarray technology) that enables rapid, unbiased discovery of both pathogen and host players that are involved in pathogen-host interactions for human infectious diseases in a high throughput manner.
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Affiliation(s)
- Yingzhu Feng
- Key Laboratory of Bio-theological Science and Technology of Ministry of Education, College of Bioengineering , Chongqing University , Chongqing 400030 , PR China.,Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management , Tainan City 701 , Taiwan.,Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Biomedical Science and Engineering , National Central University , Taoyuan City 32001 , Taiwan
| | - Jessica Ho
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Donna Pearce
- Division of Pediatric Infectious Diseases, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Shaohui Hu
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Bochu Wang
- Key Laboratory of Bio-theological Science and Technology of Ministry of Education, College of Bioengineering , Chongqing University , Chongqing 400030 , PR China
| | - Prashant Desai
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21231 , United States
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21287 , United States
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
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15
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Baldi A, Chaudhary M, Sethi S, Abhiav, Chandra R, Madan J. Armamentarium of nanoscaled lipid drug delivery systems customized for oral administration: In silico docking patronage, absorption phenomenon, preclinical status, clinical status and future prospects. Colloids Surf B Biointerfaces 2018; 170:637-647. [PMID: 29986259 DOI: 10.1016/j.colsurfb.2018.06.061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/12/2018] [Accepted: 06/27/2018] [Indexed: 02/08/2023]
Abstract
Poor drug solubility and bioavailability remain a significant and frequently encountered concern for pharmaceutical scientists. Nanoscaled lipid drug delivery systems (NSLDDS) have exhibited great potentials in oral delivery of poorly water-soluble drugs, primarily for lipophilic drugs, with several successful clinical products. In the past few years, we have find out that optimized composition of drug in lipid, surfactant, or mixture of lipid and surfactant omits the solubility, permeability and bioavailability issues, which are potential limitations for oral absorption of poorly water-soluble drugs. Lipids not only vary in structures and physiochemical properties, but also in their digestibility and absorption pathway; therefore selection of lipid excipients and dosage form has a pronounced effect on biopharmaceutical aspects of drug absorption and distribution both in vitro and in vivo. Therefore, in current critical review, a comprehensive overview of the different lipid based nanostructured drug delivery systems intended for oral administration has been presented. In addition, implication of in silico docking in designing of NSLDDS as well as mechanism of absorption of different lipid based nanoformulations through intestinal absorption window has also been offered. Moreover, attention has also been paid to NSLDDS that are currently undergoing preclinical or clinical analysis.
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Affiliation(s)
- Ashish Baldi
- Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, Punjab, India
| | - Monika Chaudhary
- Department of Medicinal Chemistry, Hindu College of Pharmacy, Sonepat, Haryana, India
| | - Sheshank Sethi
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, India
| | - Abhiav
- Division of Informatics, Systems and Research Management, Indian Council of Medical Research, New Delhi, India
| | - Ramesh Chandra
- Dr B.R Ambedkar Centre for Biomedical Research, University of Delhi, Delhi, India; Department of Chemistry, University of Delhi, Delhi, India
| | - Jitender Madan
- Department of Pharmaceutics, Chandigarh College of Pharmacy, Mohali, Punjab, India.
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16
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He X, Jiang HW, Chen H, Zhang HN, Liu Y, Xu ZW, Wu FL, Guo SJ, Hou JL, Yang MK, Yan W, Deng JY, Bi LJ, Zhang XE, Tao SC. Systematic Identification of Mycobacterium tuberculosis Effectors Reveals that BfrB Suppresses Innate Immunity. Mol Cell Proteomics 2017; 16:2243-2253. [PMID: 29018126 DOI: 10.1074/mcp.ra117.000296] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter the human immune system. The effectors of Mtb play important roles in the interactions with the host. However, because of the lack of highly efficient strategies, there are only a handful of known Mtb effectors, thus hampering our understanding of Mtb pathogenesis. In this study, we probed Mtb proteome microarray with biotinylated whole-cell lysates of human macrophages, identifying 26 Mtb membrane proteins and secreted proteins that bind to macrophage proteins. Combining GST pull-down with mass spectroscopy then enabled the specific identification of all binders. We refer to this proteome microarray-based strategy as SOPHIE (Systematic unlOcking of Pathogen and Host Interacting Effectors). Detailed investigation of a novel effector identified here, the iron storage protein BfrB (Rv3841), revealed that BfrB inhibits NF-κB-dependent transcription through binding and reducing the nuclear abundance of the ribosomal protein S3 (RPS3), which is a functional subunit of NF- κB. The importance of this interaction was evidenced by the promotion of survival in macrophages of the mycobacteria, Mycobacterium smegmatis, by overexpression of BfrB. Thus, beyond demonstrating the power of SOPHIE in the discovery of novel effectors of human pathogens, we expect that the set of Mtb effectors identified in this work will greatly facilitate the understanding of the pathogenesis of Mtb, possibly leading to additional potential molecular targets in the battle against tuberculosis.
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Affiliation(s)
- Xiang He
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - He-Wei Jiang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yin Liu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Wei Xu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan-Lin Wu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing-Li Hou
- ¶Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming-Kun Yang
- ‖Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Yan
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao-Yu Deng
- **State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Li-Jun Bi
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,§§School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China
| | - Xian-En Zhang
- ‡‡National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding; RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; .,§School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,¶¶State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China
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17
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Becton M, Averett R, Wang X. Effects of nanobubble collapse on cell membrane integrity. JOURNAL OF MICROMECHANICS AND MOLECULAR PHYSICS 2017; 2:1750008. [PMID: 29863153 PMCID: PMC5975966 DOI: 10.1142/s2424913017500084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent studies have shown that ultrasound is used to open drug-carrying liposomes to release their payloads; however, a shockwave energetic enough to rupture lipid membranes can cause collateral damage to surrounding cells. Similarly, a destructive shockwave, which may be used to rupture a cell membrane in order to lyse the cell (e.g., as in cancer treatments) may also impair or destroy nearby healthy tissue. To address this problem, we use dissipative particle dynamic (DPD) simulation to investigate the addition of a cavitation bubble between the shockwave and the model cell membrane to alter the shockwave front, allowing low-velocity shockwaves to specifically damage an intended target. We focus specifically on a spherical lipid bilayer model, and note the effect of shockwave velocity, bubble size, and orientation on the damage to the model cell. We show that a cavitation bubble greatly decreases the necessary shockwave velocity required to damage the lipid bilayer and rupture the model cell. The cavitation bubble focuses the kinetic energy of the shockwave front into a smaller area, inducing penetration at the edge of the model cell. With this work, we provide a comprehensive approach to the intricacies of model cell destruction via shockwave impact, and hope to offer a guideline for initiating targeted cellular destruction using induced cavitation bubbles and low-velocity shockwaves.
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Affiliation(s)
- Matthew Becton
- College of Engineering, University of Georgia Athens, GA 30602, USA
| | - Rodney Averett
- College of Engineering, University of Georgia Athens, GA 30602, USA
| | - Xianqiao Wang
- College of Engineering, University of Georgia Athens, GA 30602, USA
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18
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Neiswinger J, Uzoma I, Cox E, Rho H, Song G, Paul C, Jeong JS, Lu KY, Chen CS, Zhu H. Protein Microarrays: Flexible Tools for Scientific Innovation. Cold Spring Harb Protoc 2016; 2016:2016/10/pdb.top081471. [PMID: 27698245 DOI: 10.1101/pdb.top081471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Protein microarrays have emerged as a powerful tool for the scientific community, and their greatest advantage lies in the fact that thousands of reactions can be performed in a parallel and unbiased manner. The first high-density protein microarray, dubbed the "yeast proteome array," consisted of approximately 5800 full-length yeast proteins and was initially used to identify protein-lipid interactions. Further assays were subsequently developed to allow measurement of protein-DNA, protein-RNA, and protein-protein interactions, as well as four well-known posttranslational modifications: phosphorylation, acetylation, ubiquitylation, and SUMOylation. In this introduction, we describe the advent of high-density protein microarrays, as well as current methods for assessing a wide variety of protein interactions and posttranslational modifications.
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Affiliation(s)
- Johnathan Neiswinger
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Ijeoma Uzoma
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Eric Cox
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - HeeSool Rho
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Corry Paul
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Jun Seop Jeong
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
| | - Kuan-Yi Lu
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Center for High-Throughput Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland 21287
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19
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Kaminska J, Rzepnikowska W, Polak A, Flis K, Soczewka P, Bala K, Sienko M, Grynberg M, Kaliszewski P, Urbanek A, Ayscough K, Zoladek T. Phosphatidylinositol-3-phosphate regulates response of cells to proteotoxic stress. Int J Biochem Cell Biol 2016; 79:494-504. [PMID: 27498190 DOI: 10.1016/j.biocel.2016.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/29/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022]
Abstract
Human Nedd4 ubiquitin ligase, or its variants, inhibit yeast cell growth by disturbing the actin cytoskeleton organization and dynamics, and lead to an increase in levels of ubiquitinated proteins. In a screen for multicopy suppressors which rescue growth of yeast cells producing Nedd4 ligase with an inactive WW4 domain (Nedd4w4), we identified a fragment of ATG2 gene encoding part of the Atg2 core autophagy protein. Expression of the Atg2-C1 fragment (aa 1074-1447) improved growth, actin cytoskeleton organization, but did not significantly change the levels of ubiquitinated proteins in these cells. The GFP-Atg2-C1 protein in Nedd4w4-producing cells primarily localized to a single defined structure adjacent to the vacuole, surrounded by an actin filament ring, containing Hsp42 and Hsp104 chaperones. This localization was not affected in several atg deletion mutants, suggesting that it might be distinct from the phagophore assembly site (PAS). However, deletion of ATG18 encoding a phosphatidylinositol-3-phosphate (PI3P)-binding protein affected the morphology of the GFP-Atg2-C1 structure while deletion of ATG14 encoding a subunit of PI3 kinase suppressed toxicity of Nedd4w4 independently of GFP-Atg2-C1. Further analysis of the Atg2-C1 revealed that it contains an APT1 domain of previously uncharacterized function. Most importantly, we showed that this domain is able to bind phosphatidylinositol phosphates, especially PI3P, which is abundant in the PAS and endosomes. Together our results suggest that human Nedd4 ubiquitinates proteins in yeast and causes proteotoxic stress and, with some Atg proteins, leads to formation of a perivacuolar structure, which may be involved in sequestration, aggregation or degradation of proteins.
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Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Weronika Rzepnikowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Anna Polak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Krzysztof Flis
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Bala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marzena Sienko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Kaliszewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Agnieszka Urbanek
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Kathryn Ayscough
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
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20
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Yu X, Petritis B, LaBaer J. Advancing translational research with next-generation protein microarrays. Proteomics 2016; 16:1238-50. [PMID: 26749402 PMCID: PMC7167888 DOI: 10.1002/pmic.201500374] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/23/2015] [Accepted: 01/04/2016] [Indexed: 01/14/2023]
Abstract
Protein microarrays are a high-throughput technology used increasingly in translational research, seeking to apply basic science findings to enhance human health. In addition to assessing protein levels, posttranslational modifications, and signaling pathways in patient samples, protein microarrays have aided in the identification of potential protein biomarkers of disease and infection. In this perspective, the different types of full-length protein microarrays that are used in translational research are reviewed. Specific studies employing these microarrays are presented to highlight their potential in finding solutions to real clinical problems. Finally, the criteria that should be considered when developing next-generation protein microarrays are provided.
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Affiliation(s)
- Xiaobo Yu
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein Sciences (The PHOENIX Center, Beijing)BeijingP. R. China
- The Virginia G. Piper Center for Personalized DiagnosticsBiodesign InstituteArizona State UniversityTempeAZUSA
| | - Brianne Petritis
- The Virginia G. Piper Center for Personalized DiagnosticsBiodesign InstituteArizona State UniversityTempeAZUSA
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized DiagnosticsBiodesign InstituteArizona State UniversityTempeAZUSA
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21
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Farmaki T. Use of a Phosphatidylinositol Phosphate Affinity Chromatography (PIP Chromatography) for the Isolation of Proteins Involved in Protein Quality Control and Proteostasis Mechanisms in Plants. Methods Mol Biol 2016; 1450:223-232. [PMID: 27424758 DOI: 10.1007/978-1-4939-3759-2_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Protein functionality depends directly on its accurately defined three-dimensional organization, correct and efficient posttranslational modification, and transport. However, proteins are continuously under a hostile environment threatening with folding aberrations, aggregation, and mistargeting. Therefore, proteins must be constantly "followed up" by a tightly regulated homeostatic mechanism specifically known as proteostasis. To this end other proteins ensure this close surveillance including chaperones as well as structural and functional members of the proteolytic mechanisms, mainly the autophagy and the proteasome related. They accomplish their action via interactions not only with other proteins but also with lipids as well as cytoskeletal components. We describe a protocol based on an affinity chromatographic approach aiming at the isolation of phosphatidyl inositol phosphate binding proteins, a procedure which results into the enrichment and purification of several members of the proteostasis mechanism, e.g. autophagy and proteasome, among other components of the cell signaling pathways.
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Affiliation(s)
- T Farmaki
- CE.R.T.H.-IN.A.B., 6th km Charilaou-Thermi Rd., Thessaloniki, 570 01, Greece.
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22
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Saliba AE, Vonkova I, Gavin AC. The systematic analysis of protein-lipid interactions comes of age. Nat Rev Mol Cell Biol 2015; 16:753-61. [PMID: 26507169 DOI: 10.1038/nrm4080] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lipids tailor membrane identities and function as molecular hubs in all cellular processes. However, the ways in which lipids modulate protein function and structure are poorly understood and still require systematic investigation. In this Innovation article, we summarize pioneering technologies, including lipid-overlay assays, lipid pull-down assays, affinity-purification lipidomics and the liposome microarray-based assay (LiMA), that will enable protein-lipid interactions to be deciphered on a systems level. We discuss how these technologies can be applied to the charting of system-wide networks and to the development of new pharmaceutical strategies.
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Affiliation(s)
- Antoine-Emmanuel Saliba
- Institute for Molecular Infection Biology and Core Unit Systems Medicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Ivana Vonkova
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit and Molecular Medicine Partnership Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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Hu C, Huang W, Chen H, Song G, Li P, Shan Q, Zhang X, Zhang F, Zhu H, Wu L, Li Y. Autoantibody profiling on human proteome microarray for biomarker discovery in cerebrospinal fluid and sera of neuropsychiatric lupus. PLoS One 2015; 10:e0126643. [PMID: 25954975 PMCID: PMC4425696 DOI: 10.1371/journal.pone.0126643] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/04/2015] [Indexed: 11/19/2022] Open
Abstract
Autoantibodies in cerebrospinal fluid (CSF) from patients with neuropsychiatric systemic lupus erythematosus (NPSLE) may be potential biomarkers for prediction, diagnosis, or prognosis of NPSLE. We used a human proteome microarray with~17,000 unique full-length human proteins to investigate autoantibodies associated with NPSLE. Twenty-nine CSF specimens from 12 NPSLE, 7 non-NPSLE, and 10 control (non-systemic lupus erythematosus)patients were screened for NPSLE-associated autoantibodies with proteome microarrays. A focused autoantigen microarray of candidate NPSLE autoantigens was applied to profile a larger cohort of CSF with patient-matched sera. We identified 137 autoantigens associated with NPSLE. Ingenuity Pathway Analysis revealed that these autoantigens were enriched for functions involved in neurological diseases (score = 43).Anti-proliferating cell nuclear antigen (PCNA) was found in the CSF of NPSLE and non-NPSLE patients. The positive rates of 4 autoantibodies in CSF specimens were significantly different between the SLE (i.e., NPSLE and non-NPSLE) and control groups: anti-ribosomal protein RPLP0, anti-RPLP1, anti-RPLP2, and anti-TROVE2 (also known as anti-Ro/SS-A). The positive rate for anti-SS-A associated with NPSLE was higher than that for non-NPSLE (31.11% cf. 10.71%; P = 0.045).Further analysis showed that anti-SS-A in CSF specimens was related to neuropsychiatric syndromes of the central nervous system in SLE (P = 0.009). Analysis with Spearman’s rank correlation coefficient indicated that the titers of anti-RPLP2 and anti-SS-A in paired CSF and serum specimens significantly correlated. Human proteome microarrays offer a powerful platform to discover novel autoantibodies in CSF samples. Anti-SS-A autoantibodies may be potential CSF markers for NPSLE.
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Affiliation(s)
- Chaojun Hu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Wei Huang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Hua Chen
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Guang Song
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ping Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Qiang Shan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xuan Zhang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Fengchun Zhang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (YZL); (LW); (HZ)
| | - Lin Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (YZL); (LW); (HZ)
| | - Yongzhe Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China
- * E-mail: (YZL); (LW); (HZ)
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24
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Wu L, Chen X, Mei Y, Hong Q, Feng Z, Lv Y, Wen J, Liu X, Cai G, Chen X. CXCL10 expression induced by Mxi1 inactivation induces mesangial cell apoptosis in mouse Habu nephritis. Cell Signal 2015; 27:943-50. [PMID: 25683914 DOI: 10.1016/j.cellsig.2015.01.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/13/2015] [Accepted: 01/27/2015] [Indexed: 11/18/2022]
Abstract
MAX interactor 1 (Mxi1) proteins are c-myc antagonists that primarily exert their biological functions by inhibiting Myc-dependent gene transcription. In this study, Mxi1(-/-) mice were used to generate a model of mesangial proliferative glomerulonephritis for the first time. In the present study, we demonstrated that Mxi1(-/-) mice exhibited a more typical and severe pathological phenotype, which was displayed primarily as a noticeable dissolution phenotype with a higher proportion of apoptotic cells and higher chemokine CXCL10 expression during the early days of modeling, compared with wild-type mice. Additionally, we determined that IRF3-mediated TLR4 signaling was likely involved in regulating CXCL10 expression, which might participate in the mesangial dissolution process. We also found increases in CXCL10 expression, caspase 3 activation, and the proportion of apoptotic cells when Mxi1 expression was inhibited in mouse mesangial cells. Furthermore, the proportion of apoptotic cells decreased after inhibiting CXCL10 expression. Therefore, we concluded that the mesangial cell apoptosis observed in this mesangial proliferative glomerulonephritis model was related to CXCL10 expression induced by Mxi1 inactivation. This finding provides a new theoretical basis for the mechanism of mesangial proliferative glomerulonephritis progression and reveals potential intervention targets for the early treatment of this disease.
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Affiliation(s)
- Lingling Wu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China; Medical College, NanKai University, Tianjin, China
| | - Xiaoniao Chen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China; Medical College, NanKai University, Tianjin, China
| | - Yan Mei
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China
| | - Quan Hong
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China
| | - Zhe Feng
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China
| | - Yang Lv
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China
| | - Jun Wen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China
| | - Xiaoluan Liu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China
| | - Guangyan Cai
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China.
| | - Xiangmei Chen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, China.
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Angerer H. Eukaryotic LYR Proteins Interact with Mitochondrial Protein Complexes. BIOLOGY 2015; 4:133-50. [PMID: 25686363 PMCID: PMC4381221 DOI: 10.3390/biology4010133] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/04/2015] [Indexed: 01/18/2023]
Abstract
In eukaryotic cells, mitochondria host ancient essential bioenergetic and biosynthetic pathways. LYR (leucine/tyrosine/arginine) motif proteins (LYRMs) of the Complex1_LYR-like superfamily interact with protein complexes of bacterial origin. Many LYR proteins function as extra subunits (LYRM3 and LYRM6) or novel assembly factors (LYRM7, LYRM8, ACN9 and FMC1) of the oxidative phosphorylation (OXPHOS) core complexes. Structural insights into complex I accessory subunits LYRM6 and LYRM3 have been provided by analyses of EM and X-ray structures of complex I from bovine and the yeast Yarrowia lipolytica, respectively. Combined structural and biochemical studies revealed that LYRM6 resides at the matrix arm close to the ubiquinone reduction site. For LYRM3, a position at the distal proton-pumping membrane arm facing the matrix space is suggested. Both LYRMs are supposed to anchor an acyl-carrier protein (ACPM) independently to complex I. The function of this duplicated protein interaction of ACPM with respiratory complex I is still unknown. Analysis of protein-protein interaction screens, genetic analyses and predicted multi-domain LYRMs offer further clues on an interaction network and adaptor-like function of LYR proteins in mitochondria.
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Affiliation(s)
- Heike Angerer
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Street 9, Frankfurt am Main 60438, Germany.
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26
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Mycobacterium tuberculosis proteome microarray for global studies of protein function and immunogenicity. Cell Rep 2014; 9:2317-29. [PMID: 25497094 DOI: 10.1016/j.celrep.2014.11.023] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/17/2014] [Accepted: 11/17/2014] [Indexed: 12/30/2022] Open
Abstract
Poor understanding of the basic biology of Mycobacterium tuberculosis (MTB), the etiological agent of tuberculosis, hampers development of much-needed drugs, vaccines, and diagnostic tests. Better experimental tools are needed to expedite investigations of this pathogen at the systems level. Here, we present a functional MTB proteome microarray covering most of the proteome and an ORFome library. We demonstrate the broad applicability of the microarray by investigating global protein-protein interactions, small-molecule-protein binding, and serum biomarker discovery, identifying 59 PknG-interacting proteins, 30 bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding proteins, and 14 MTB proteins that together differentiate between tuberculosis (TB) patients with active disease and recovered individuals. Results suggest that the MTB rhamnose pathway is likely regulated by both the serine/threonine kinase PknG and c-di-GMP. This resource has the potential to generate a greater understanding of key biological processes in the pathogenesis of tuberculosis, possibly leading to more effective therapies for the treatment of this ancient disease.
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Lv Y, Cai G, Chen X. Applications of urinary proteomics in renal disease research using animal models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 845:145-50. [PMID: 25355577 DOI: 10.1007/978-94-017-9523-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Animal models of renal disease are essential tools in research on kidney disease and have provided valuable insights into pathogenesis. Use of animal models minimises inter-individual differences, allows specific pathological changes to be examined, and facilitates collection of tissue samples. Thus, mechanistic research and identification of biomarkers are possible. Various animal models manifesting specific pathological lesions can be used to investigate acute or chronic kidney disease (CKD). Urine, a terminal metabolic product, is produced via glomerular filtration, reabsorption, and excretion in the tubular and collecting ducts, reflecting the functions of glomeruli or tubular tissue stimulated in various ways or subject to disease. Almost 70 % of urinary proteins originate from the kidney (the other 30 % come from plasma), and urinary sampling is important to noninvasively detect renal disease. Proteomics is powerful when used to screen urine components. Increasingly, urine proteomics is used to explore the pathogenesis of kidney disease in animals and to identify novel biomarkers of renal disease. In this section, we will introduce the field of urinary proteomics as applied in different models of animal renal disease and the valuable role played by proteomics in noninvasive diagnosis and rational treatment of human renal disease.
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Affiliation(s)
- Yang Lv
- Department of Nephrology, Chinese PLA General Hospital, State Key Laboratory of Kidney Disease (2011DAV00088), National Clinical Research Center for Kidney Disease (2013BAI09B05), Fuxing Road 28, Beijing, 100853, People's Republic of China
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28
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Best MD. Global approaches for the elucidation of phosphoinositide-binding proteins. Chem Phys Lipids 2013; 182:19-28. [PMID: 24220499 DOI: 10.1016/j.chemphyslip.2013.10.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/13/2013] [Accepted: 10/29/2013] [Indexed: 12/22/2022]
Abstract
Phosphoinositide lipids (PIPns) control numerous critical biological pathways, typically through the regulation of protein function driven by non-covalent protein-lipid binding interactions. Despite the importance of these systems, the unraveling of the full scope of protein-PIPn interactions has represented a significant challenge due to the massive complexity associated with these events, including the large number of diverse proteins that bind to these lipids, variations in the mechanisms by which proteins bind to lipids, and the presence of multiple distinct PIPn isomers. As a result of this complexity, global methods in which numerous proteins that bind PIPns can be identified and characterized simultaneously from complex samples, which have been enabled by key technological advancements, have become popular as an efficient means for tackling this challenge. This review article provides an overview of advancements in large-scale methods for profiling protein-PIPn binding, including experimental methods, such as affinity enrichment, microarray analysis and activity-based protein profiling, as well as computational methods, and combined computational/experimental efforts.
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Affiliation(s)
- Michael D Best
- Department of Chemistry, The University of Tennessee, 1420 Circle Drive, Knoxville, TN 37996, United States.
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29
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Oxley D, Ktistakis N, Farmaki T. Differential isolation and identification of PI(3)P and PI(3,5)P2 binding proteins from Arabidopsis thaliana using an agarose-phosphatidylinositol-phosphate affinity chromatography. J Proteomics 2013; 91:580-94. [PMID: 24007659 DOI: 10.1016/j.jprot.2013.08.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/25/2013] [Accepted: 08/20/2013] [Indexed: 12/13/2022]
Abstract
UNLABELLED A phosphatidylinositol-phosphate affinity chromatographic approach combined with mass spectrometry was used in order to identify novel PI(3)P and PI(3,5)P2 binding proteins from Arabidopsis thaliana suspension cell extracts. Most of the phosphatidylinositol-phosphate interacting candidates identified from this differential screening are characterized by lysine/arginine rich patches. Direct phosphoinositide binding was identified for important membrane trafficking regulators as well as protein quality control proteins such as the ATG18p orthologue involved in autophagosome formation and the lipid Sec14p like transfer protein. A pentatricopeptide repeat (PPR) containing protein was shown to directly bind to PI(3,5)P2 but not to PI(3)P. PIP chromatography performed using extracts obtained from high salt (0.4M and 1M NaCl) pretreated suspensions showed that the association of an S5-1 40S ribosomal protein with both PI(3)P and PI(3,5)P2 was abolished under salt stress whereas salinity stress induced an increase in the phosphoinositide association of the DUF538 domain containing protein SVB, associated with trichome size. Additional interacting candidates were co-purified with the phosphoinositide bound proteins. Binding of the COP9 signalosome, the heat shock proteins, and the identified 26S proteasomal subunits, is suggested as an indirect effect of their interaction with other proteins directly bound to the PI(3)P and the PI(3,5)P2 phosphoinositides. BIOLOGICAL SIGNIFICANCE PI(3,5)P2 is of special interest because of its low abundance. Furthermore, no endogenous levels have yet been detected in A. thaliana (although there is evidence for its existence in plants). Therefore the isolation of novel interacting candidates in vitro would be of a particular importance since the future study and localization of the respective endogenous proteins may indicate possible targeted compartments or tissues where PI(3,5)P2 could be enriched and thereafter identified. In addition, PI(3,5)P2 is a phosphoinositide extensively studied in mammalian and yeast systems. However, our knowledge of its role in plants as well as a list of its effectors from plants is very limited.
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Affiliation(s)
- David Oxley
- The Mass Spectrometry Group, Babraham Institute, Cambridge, CB2 4AT, UK
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