1
|
Song MS, Nam JH, Noh KE, Lim DS. Dendritic Cell-Based Immunotherapy: The Importance of Dendritic Cell Migration. J Immunol Res 2024; 2024:7827246. [PMID: 38628676 PMCID: PMC11019573 DOI: 10.1155/2024/7827246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
Dendritic cells (DCs) are specialized antigen-presenting cells that are crucial for maintaining self-tolerance, initiating immune responses against pathogens, and patrolling body compartments. Despite promising aspects, DC-based immunotherapy faces challenges that include limited availability, immune escape in tumors, immunosuppression in the tumor microenvironment, and the need for effective combination therapies. A further limitation in DC-based immunotherapy is the low population of migratory DC (around 5%-10%) that migrate to lymph nodes (LNs) through afferent lymphatics depending on the LN draining site. By increasing the population of migratory DCs, DC-based immunotherapy could enhance immunotherapeutic effects on target diseases. This paper reviews the importance of DC migration and current research progress in the context of DC-based immunotherapy.
Collapse
Affiliation(s)
- Min-Seon Song
- Department of Bioconvergence, Graduate School and Department of Biotechnology, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Ji-Hee Nam
- Department of Bioconvergence, Graduate School and Department of Biotechnology, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Kyung-Eun Noh
- Department of Bioconvergence, Graduate School and Department of Biotechnology, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Dae-Seog Lim
- Department of Bioconvergence, Graduate School and Department of Biotechnology, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| |
Collapse
|
2
|
Deviri D, Safran SA. Mechanosensitivity of phase separation in an elastic gel. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:16. [PMID: 38376695 PMCID: PMC10879317 DOI: 10.1140/epje/s10189-024-00405-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Liquid-liquid phase separation (LLPS) in binary or multi-component solutions is a well-studied subject in soft matter with extensive applications in biological systems. In recent years, several experimental studies focused on LLPS of solutes in hydrated gels, where the formation of coexisting domains induces elastic deformations within the gel. While the experimental studies report unique physical characteristics of these systems, such as sensitivity to mechanical forces and stabilization of multiple, periodic phase-separated domains, the theoretical understanding of such systems and the role of long-range interactions have not emphasized the nonlinear nature of the equilibrium binodal for strong segregation of the solute. In this paper, we formulate a generic, mean-field theory of a hydrated gel in the presence of an additional solute which changes the elastic properties of the gel. We derive equations for the equilibrium binodal of the phase separation of the solvent and solute and show that the deformations induced by the solute can result in effective long-range interactions between phase-separating solutes that can either enhance or, in the case of externally applied pressure, suppress phase separation of the solute relative to the case where there is no gel. This causes the coexisting concentrations at the binodal to depend on the system-wide average concentration, in contrast to the situation for phase separation in the absence of the gel.
Collapse
Affiliation(s)
- Dan Deviri
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100, Rehovot, Israel.
- Carbon Blue Ltd., 3303201, Haifa, Israel.
| | - Samuel A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100, Rehovot, Israel
| |
Collapse
|
3
|
Liu Y, Chen X, Yin S, Chang X, Lv C, Zang J, Leng X, Zhang T, Zhao G. Directed Self-Assembly of Dimeric Building Blocks into Networklike Protein Origami to Construct Hydrogels. ACS NANO 2022; 16:19472-19481. [PMID: 36315654 DOI: 10.1021/acsnano.2c09391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Engineering proteins to construct self-assemblies is of crucial significance not only for understanding the sophisticated living systems but also for fabricating advanced materials with unexplored functions. However, due to the inherent chemical heterogeneity and structural complexity of the protein surface, designing complex protein assemblies in an anisotropic fashion remains challenging. Here, we describe a self-assembly approach to fabricating protein origami with a networklike structure by designing dual noncovalent interactions on the different positions of a single protein building block. With dimeric proteins as building blocks, 1D protein filaments were constructed by the designed metal coordination at key protein interfaces. Subsequently, the network superstructures were created by the cross-linking of the 1D protein filaments at branch point linkages through the second designed π-π stacking interactions. Notably, upon increasing the protein concentration, the formed protein networks convert into hydrogels with reversible, injectable, and self-healing properties, which have the ability to promote bone regeneration. This strategy could be used to fabricate other protein-based materials with unexplored functions.
Collapse
Affiliation(s)
- Yu Liu
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Xuemin Chen
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Shuhua Yin
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Xiaoxi Chang
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Xiaojing Leng
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| |
Collapse
|
4
|
Li HL, Shan SW, Stamer WD, Li KK, Chan HHL, Civan MM, To CH, Lam TC, Do CW. Mechanistic Effects of Baicalein on Aqueous Humor Drainage and Intraocular Pressure. Int J Mol Sci 2022; 23:ijms23137372. [PMID: 35806375 PMCID: PMC9266486 DOI: 10.3390/ijms23137372] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
Elevated intraocular pressure (IOP) is a major risk factor for glaucoma that results from impeded fluid drainage. The increase in outflow resistance is caused by trabecular meshwork (TM) cell dysfunction and excessive extracellular matrix (ECM) deposition. Baicalein (Ba) is a natural flavonoid and has been shown to regulate cell contraction, fluid secretion, and ECM remodeling in various cell types, suggesting the potential significance of regulating outflow resistance and IOP. We demonstrated that Ba significantly lowered the IOP by about 5 mmHg in living mice. Consistent with that, Ba increased the outflow facility by up to 90% in enucleated mouse eyes. The effects of Ba on cell volume regulation and contractility were examined in primary human TM (hTM) cells. We found that Ba (1–100 µM) had no effect on cell volume under iso-osmotic conditions but inhibited the regulatory volume decrease (RVD) by up to 70% under hypotonic challenge. In addition, Ba relaxed hTM cells via reduced myosin light chain (MLC) phosphorylation. Using iTRAQ-based quantitative proteomics, 47 proteins were significantly regulated in hTM cells after a 3-h Ba treatment. Ba significantly increased the expression of cathepsin B by 1.51-fold and downregulated the expression of D-dopachrome decarboxylase and pre-B-cell leukemia transcription factor-interacting protein 1 with a fold-change of 0.58 and 0.40, respectively. We suggest that a Ba-mediated increase in outflow facility is triggered by cell relaxation via MLC phosphorylation along with inhibiting RVD in hTM cells. The Ba-mediated changes in protein expression support the notion of altered ECM homeostasis, potentially contributing to a reduction of outflow resistance and thereby IOP.
Collapse
Affiliation(s)
- Hoi-lam Li
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong; (H.-l.L.); (S.W.S.); (K.-k.L.); (H.H.-l.C.); (C.-h.T.); (T.C.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong
| | - Sze Wan Shan
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong; (H.-l.L.); (S.W.S.); (K.-k.L.); (H.H.-l.C.); (C.-h.T.); (T.C.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong
- Research Centre for Chinese Medicine Innovation (RCMI), The Hong Kong Polytechnic University, Hong Kong
| | - W. Daniel Stamer
- Department of Ophthalmology, Duke University, Durham, NC 27708, USA;
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - King-kit Li
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong; (H.-l.L.); (S.W.S.); (K.-k.L.); (H.H.-l.C.); (C.-h.T.); (T.C.L.)
| | - Henry Ho-lung Chan
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong; (H.-l.L.); (S.W.S.); (K.-k.L.); (H.H.-l.C.); (C.-h.T.); (T.C.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong
- Research Centre for Chinese Medicine Innovation (RCMI), The Hong Kong Polytechnic University, Hong Kong
| | - Mortimer M. Civan
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Chi-ho To
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong; (H.-l.L.); (S.W.S.); (K.-k.L.); (H.H.-l.C.); (C.-h.T.); (T.C.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong
- Research Centre for Chinese Medicine Innovation (RCMI), The Hong Kong Polytechnic University, Hong Kong
| | - Thomas Chuen Lam
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong; (H.-l.L.); (S.W.S.); (K.-k.L.); (H.H.-l.C.); (C.-h.T.); (T.C.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong
- Research Centre for Chinese Medicine Innovation (RCMI), The Hong Kong Polytechnic University, Hong Kong
| | - Chi-wai Do
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong; (H.-l.L.); (S.W.S.); (K.-k.L.); (H.H.-l.C.); (C.-h.T.); (T.C.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong
- Research Centre for Chinese Medicine Innovation (RCMI), The Hong Kong Polytechnic University, Hong Kong
- Research Institute of Smart Ageing (RISA), The Hong Kong Polytechnic University, Hong Kong
- Correspondence:
| |
Collapse
|
5
|
Role of ARP2/3 Complex-Driven Actin Polymerization in RSV Infection. Pathogens 2021; 11:pathogens11010026. [PMID: 35055974 PMCID: PMC8781601 DOI: 10.3390/pathogens11010026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/30/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading viral agent causing bronchiolitis and pneumonia in children under five years old worldwide. The RSV infection cycle starts with macropinocytosis-based entry into the host airway epithelial cell membrane, followed by virus transcription, replication, assembly, budding, and spread. It is not surprising that the host actin cytoskeleton contributes to different stages of the RSV replication cycle. RSV modulates actin-related protein 2/3 (ARP2/3) complex-driven actin polymerization for a robust filopodia induction on the infected lung epithelial A549 cells, which contributes to the virus’s budding, and cell-to-cell spread. Thus, a comprehensive understanding of RSV-induced cytoskeletal modulation and its role in lung pathobiology may identify novel intervention strategies. This review will focus on the role of the ARP2/3 complex in RSV’s pathogenesis and possible therapeutic targets to the ARP2/3 complex for RSV.
Collapse
|
6
|
Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021. [PMID: 34185516 DOI: 10.1101/2021.02.24.432456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
Collapse
Affiliation(s)
| | - Federico Fanalista
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | | |
Collapse
|
7
|
Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021; 10:1690-1702. [PMID: 34185516 PMCID: PMC8291763 DOI: 10.1021/acssynbio.1c00068] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Indexed: 12/17/2022]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
Collapse
Affiliation(s)
| | - Federico Fanalista
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department
of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | | |
Collapse
|
8
|
Keller-Pinter A, Gyulai-Nagy S, Becsky D, Dux L, Rovo L. Syndecan-4 in Tumor Cell Motility. Cancers (Basel) 2021; 13:cancers13133322. [PMID: 34282767 PMCID: PMC8268284 DOI: 10.3390/cancers13133322] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Cell migration is crucial fReaor metastasis formation and a hallmark of malignancy. The primary cause of high mortality among oncology patients is the ability of cancer cells to metastasize. To form metastasis, primary tumor cells must be intrinsically able to move. The transmembrane, heparan sulfate proteoglycan syndecan-4 (SDC4) exhibits multiple functions in signal transduction by regulating Rac1 GTPase activity and consequently actin remodeling, as well as regulating focal adhesion kinase, protein kinase C-alpha and the level of intracellular calcium. By affecting several signaling pathways and biological processes, SDC4 is involved in cell migration under physiological and pathological conditions as well. In this review, we discuss the SDC4-mediated cell migration focusing on the role of SDC4 in tumor cell movement. Abstract Syndecan-4 (SDC4) is a ubiquitously expressed, transmembrane proteoglycan bearing heparan sulfate chains. SDC4 is involved in numerous inside-out and outside-in signaling processes, such as binding and sequestration of growth factors and extracellular matrix components, regulation of the activity of the small GTPase Rac1, protein kinase C-alpha, the level of intracellular calcium, or the phosphorylation of focal adhesion kinase. The ability of this proteoglycan to link the extracellular matrix and actin cytoskeleton enables SDC4 to contribute to biological functions like cell adhesion and migration, cell proliferation, cytokinesis, cellular polarity, or mechanotransduction. The multiple roles of SDC4 in tumor pathogenesis and progression has already been demonstrated; therefore, the expression and signaling of SDC4 was investigated in several tumor types. SDC4 influences tumor progression by regulating cell proliferation as well as cell migration by affecting cell-matrix adhesion and several signaling pathways. Here, we summarize the general role of SDC4 in cell migration and tumor cell motility.
Collapse
Affiliation(s)
- Aniko Keller-Pinter
- Department of Biochemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary; (S.G.-N.); (D.B.); (L.D.)
- Correspondence:
| | - Szuzina Gyulai-Nagy
- Department of Biochemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary; (S.G.-N.); (D.B.); (L.D.)
| | - Daniel Becsky
- Department of Biochemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary; (S.G.-N.); (D.B.); (L.D.)
| | - Laszlo Dux
- Department of Biochemistry, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary; (S.G.-N.); (D.B.); (L.D.)
| | - Laszlo Rovo
- Department of Oto-Rhino-Laryngology and Head-Neck Surgery, University of Szeged, H-6725 Szeged, Hungary;
| |
Collapse
|
9
|
Baltussen TJH, Coolen JPM, Verweij PE, Dijksterhuis J, Melchers WJG. Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics. J Fungi (Basel) 2021; 7:270. [PMID: 33916245 PMCID: PMC8067318 DOI: 10.3390/jof7040270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.
Collapse
Affiliation(s)
- Tim J. H. Baltussen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| |
Collapse
|
10
|
Rogers CM, Sanders E, Nguyen PA, Smith-Kinnaman W, Mosley AL, Bochman ML. The Genetic and Physical Interactomes of the Saccharomyces cerevisiae Hrq1 Helicase. G3 (BETHESDA, MD.) 2020; 10:4347-4357. [PMID: 33115721 PMCID: PMC7718736 DOI: 10.1534/g3.120.401864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/23/2020] [Indexed: 01/03/2023]
Abstract
The human genome encodes five RecQ helicases (RECQL1, BLM, WRN, RECQL4, and RECQL5) that participate in various processes underpinning genomic stability. Of these enzymes, the disease-associated RECQL4 is comparatively understudied due to a variety of technical challenges. However, Saccharomyces cerevisiae encodes a functional homolog of RECQL4 called Hrq1, which is more amenable to experimentation and has recently been shown to be involved in DNA inter-strand crosslink (ICL) repair and telomere maintenance. To expand our understanding of Hrq1 and the RecQ4 subfamily of helicases in general, we took a multi-omics approach to define the Hrq1 interactome in yeast. Using synthetic genetic array analysis, we found that mutations of genes involved in processes such as DNA repair, chromosome segregation, and transcription synthetically interact with deletion of HRQ1 and the catalytically inactive hrq1-K318A allele. Pull-down of tagged Hrq1 and mass spectrometry identification of interacting partners similarly underscored links to these processes and others. Focusing on transcription, we found that hrq1 mutant cells are sensitive to caffeine and that mutation of HRQ1 alters the expression levels of hundreds of genes. In the case of hrq1-K318A, several of the most highly upregulated genes encode proteins of unknown function whose expression levels are also increased by DNA ICL damage. Together, our results suggest a heretofore unrecognized role for Hrq1 in transcription, as well as novel members of the Hrq1 ICL repair pathway. These data expand our understanding of RecQ4 subfamily helicase biology and help to explain why mutations in human RECQL4 cause diseases of genomic instability.
Collapse
Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| | - Elsbeth Sanders
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| | - Phoebe A Nguyen
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| | - Whitney Smith-Kinnaman
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405
| |
Collapse
|
11
|
Le Guernic A, Geffard A, Rioult D, Bigot-Clivot A, Leprêtre M, Palos Ladeiro M. Cellular and molecular complementary immune stress markers for the model species Dreissena polymorpha. FISH & SHELLFISH IMMUNOLOGY 2020; 107:452-462. [PMID: 33197585 DOI: 10.1016/j.fsi.2020.10.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/25/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to combine cellular and molecular analyses for better detail the effects of various stresses on a sentinel species of freshwater invertebrate. For this purpose, the hemocytes of the zebra mussel, Dreissena polymorpha, were exposed to different stresses at two different intensities, high or low: chemical (cadmium and ionomycin), physical (ultraviolet B), or biological ones (Cryptosporidium parvum and Toxoplasma gondii). After exposure, flow cytometry and droplet digital PCR analyses were performed on the same pools of hemocytes. Several responses related to necrosis, apoptosis, phagocytosis, production of nitric oxide and expression level of several genes related to the antioxidant, detoxification and immune systems were evaluated. Results showed that hemocyte integrity was compromised by both chemical and physical stress, and cellular markers of phagocytosis reacted to ionomycin and protozoa. While cadmium induced oxidative stress and necrosis, ionomycin tends to modulate the immune response of hemocytes. Although both biological stresses led to a similar immune response, C. parvum oocysts induced more effects than T. gondii, notably through the expression of effector caspases gene and an increase in hemocyte necrosis. This suggests different management of the two protozoa by the cell. This work provides new knowledge of biomarkers in the zebra mussel, at both cellular and molecular levels, and contributes to elucidate the mechanisms of action of different kinds of stress in this species.
Collapse
Affiliation(s)
- Antoine Le Guernic
- Reims Champagne-Ardenne University (URCA), Campus Moulin de La Housse, UMR-I02 SEBIO, 51687, Reims, France.
| | - Alain Geffard
- Reims Champagne-Ardenne University (URCA), Campus Moulin de La Housse, UMR-I02 SEBIO, 51687, Reims, France
| | - Damien Rioult
- Reims Champagne-Ardenne University (URCA), Campus Moulin de La Housse, UMR-I02 SEBIO, 51687, Reims, France; Plateau Technique Mobile en Cytométrie Environnementale MOBICYTE, URCA/INERIS, URCA, 51687, Reims, France
| | - Aurélie Bigot-Clivot
- Reims Champagne-Ardenne University (URCA), Campus Moulin de La Housse, UMR-I02 SEBIO, 51687, Reims, France
| | - Maxime Leprêtre
- Reims Champagne-Ardenne University (URCA), Campus Moulin de La Housse, UMR-I02 SEBIO, 51687, Reims, France
| | - Mélissa Palos Ladeiro
- Reims Champagne-Ardenne University (URCA), Campus Moulin de La Housse, UMR-I02 SEBIO, 51687, Reims, France
| |
Collapse
|
12
|
Zhang J, Li Y, Zhao S, Wu X. Identification of A functional region in Bombyx mori nucleopolyhedrovirus VP39 that is essential for nuclear actin polymerization. Virology 2020; 550:37-50. [PMID: 32877775 DOI: 10.1016/j.virol.2020.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 02/03/2023]
Abstract
Nuclear actin polymerization plays an indispensable role in the nuclear assembly of baculovirus nucleocapsid, but the underlying viral infection-mediated mechanism remains unclear. VP39 is the major protein in baculovirus capsid, which builds the skeleton of the capsid tubular structure. VP39 is suggested in previous studies to interact with cellular actin and mediate actin polymerization. However, it is unclear about the role of VP39 in mediating nuclear actin polymerization. Results in this study indicated that vp39 deletion abolished nuclear actin polymerization, which was recovered after vp39 repair, revealing the essential part of VP39 in nuclear actin polymerization. Furthermore, a series of mutants with vp39 deletions were constructed to analyze the important region responsible for nuclear actin polymerization. In addition, intracellular localization analysis demonstrated that the amino acids 192-286 in VP39 C-terminal are responsible for nuclear actin polymerization.
Collapse
Affiliation(s)
- Jianjia Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yang Li
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shudi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
13
|
Marín-Garzón NA, Magalhães AFB, Mota LFM, Fonseca LFS, Chardulo LAL, Albuquerque LG. Genome-wide association study identified genomic regions and putative candidate genes affecting meat color traits in Nellore cattle. Meat Sci 2020; 171:108288. [PMID: 32949820 DOI: 10.1016/j.meatsci.2020.108288] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 01/08/2023]
Abstract
Single and multiple-trait GWAS were conducted to detect genomic regions and candidate genes associated with meat color traits (L*, lightness; a*, redness; b*, yellowness) in Nellore cattle. Phenotypic records of 5000 animals, and 3794 genotypes for 614,274 SNPs were used. The BLUPF90 family programs were used through single step GWAS approach. The top 10 genomic regions from single-trait GWAS explained 13.64%, 15.12% and 13% of genetic variance of L*, a* and b*, which harbored 129, 70, and 84 candidate genes, respectively. Regarding multiple-trait GWAS, the top 10 SNP windows explained 17.46%, 18.98% and 13.74% of genetic variance of L*, a* and b*, and harbored 124, 86, and 82 candidate genes, respectively. Pleiotropic effects were evidenced by the overlapping regions detected on BTA 15 and 26 associated with L* and a* (genetic correlation of -0.53), and on BTA 18 associated with a* and b* (genetic correlation of 0.60). Similar genomic regions located on BTA 2, 5, 6, and 18 were detected through single and multi-trait GWAS. Overlapped regions harbored a total of 30 functional candidate genes involved in mitochondrial activity, structural integrity of muscles, lipid oxidation, anaerobic metabolism, and muscular pH.
Collapse
Affiliation(s)
- N A Marín-Garzón
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil.
| | - A F B Magalhães
- APTA Beef Cattle Center, Animal Science Institute, Sertãozinho, São Paulo, Brazil
| | - L F M Mota
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil
| | - L F S Fonseca
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil
| | - L A L Chardulo
- São Paulo State University (Unesp), College of Veterinary and Animal Science, Botucatu, SP, Brazil; National Council for Science and Technological Development (CNPq), Brasília, Brazil
| | - L G Albuquerque
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil; National Council for Science and Technological Development (CNPq), Brasília, Brazil
| |
Collapse
|
14
|
Whitelaw JA, Swaminathan K, Kage F, Machesky LM. The WAVE Regulatory Complex Is Required to Balance Protrusion and Adhesion in Migration. Cells 2020; 9:E1635. [PMID: 32646006 PMCID: PMC7407199 DOI: 10.3390/cells9071635] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
Cells migrating over 2D substrates are required to polymerise actin at the leading edge to form lamellipodia protrusions and nascent adhesions to anchor the protrusion to the substrate. The major actin nucleator in lamellipodia formation is the Arp2/3 complex, which is activated by the WAVE regulatory complex (WRC). Using inducible Nckap1 floxed mouse embryonic fibroblasts (MEFs), we confirm that the WRC is required for lamellipodia formation, and importantly, for generating the retrograde flow of actin from the leading cell edge. The loss of NCKAP1 also affects cell spreading and focal adhesion dynamics. In the absence of lamellipodium, cells can become elongated and move with a single thin pseudopod, which appears devoid of N-WASP. This phenotype was more prevalent on collagen than fibronectin, where we observed an increase in migratory speed. Thus, 2D cell migration on collagen is less dependent on branched actin.
Collapse
Affiliation(s)
| | - Karthic Swaminathan
- CRUK Beatson Institute, Glasgow G61 1BD, UK; (K.S.); (L.M.M.)
- School of Chemistry and Bioscience, University of Bradford, Bradford BD7 1PD, UK
| | - Frieda Kage
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755-3844, USA;
- Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Laura M. Machesky
- CRUK Beatson Institute, Glasgow G61 1BD, UK; (K.S.); (L.M.M.)
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| |
Collapse
|
15
|
Holliday LS, de Faria LP, Rody WJ. Actin and Actin-Associated Proteins in Extracellular Vesicles Shed by Osteoclasts. Int J Mol Sci 2019; 21:ijms21010158. [PMID: 31881680 PMCID: PMC6981389 DOI: 10.3390/ijms21010158] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) are shed by all eukaryotic cells and have emerged as important intercellular regulators. EVs released by osteoclasts were recently identified as important coupling factors in bone remodeling. They are shed as osteoclasts resorb bone and stimulate osteoblasts to form bone to replace the bone resorbed. We reported the proteomic content of osteoclast EVs with data from two-dimensional, high resolution liquid chromatography/mass spectrometry. In this article, we examine in detail the actin and actin-associated proteins found in osteoclast EVs. Like EVs from other cell types, actin and various actin-associated proteins were abundant. These include components of the polymerization machinery, myosin mechanoenzymes, proteins that stabilize or depolymerize microfilaments, and actin-associated proteins that are involved in regulating integrins. The selective incorporation of actin-associated proteins into osteoclast EVs suggests that they have roles in the formation of EVs and/or the regulatory signaling functions of the EVs. Regulating integrins so that they bind extracellular matrix tightly, in order to attach EVs to the extracellular matrix at specific locations in organs and tissues, is one potential active role for actin-associated proteins in EVs.
Collapse
Affiliation(s)
- L. Shannon Holliday
- Department of Orthodontics, College of Dentistry, University of Florida, Gainesville, FL 32610, USA
- Correspondence:
| | - Lorraine Perciliano de Faria
- Department of Biomaterials and Oral Biology, School of Dentistry, University of São Paulo, São Paulo 01000, Brazil;
| | - Wellington J. Rody
- Department of Orthodontics and Pediatric Dentistry, Stony Brook University School of Dental Medicine, Stony Brook, NY 11794, USA;
| |
Collapse
|
16
|
Cohen J, Raviv S, Adir O, Padmanabhan K, Soffer A, Luxenburg C. The Wave complex controls epidermal morphogenesis and proliferation by suppressing Wnt-Sox9 signaling. J Cell Biol 2019; 218:1390-1406. [PMID: 30867227 PMCID: PMC6446834 DOI: 10.1083/jcb.201807216] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/11/2018] [Accepted: 02/01/2019] [Indexed: 02/08/2023] Open
Abstract
The Wave complex promotes Arp2/3-mediated actin polymerization. Cohen et al. show that Wave complex activity regulates epidermal shape and growth. Without Wave complex activity, F-actin content is down-regulated and ectopic activity of the Wnt/β-catenin–SOX9 pathway is triggered. This activity induces epidermal hyperproliferation and disrupts tissue architecture. Development of the skin epidermis requires tight spatiotemporal control over the activity of several signaling pathways; however, the mechanisms that orchestrate these events remain poorly understood. Here, we identify a key role for the Wave complex proteins ABI1 and Wave2 in regulating signals that control epidermal shape and growth. In utero RNAi-mediated silencing of Abi1 or Wasf2 induced cellular hyperproliferation and defects in architecture of the interfollicular epidermis (IFE) and delayed hair follicle growth. Unexpectedly, SOX9, a hair follicle growth regulator, was aberrantly expressed throughout the IFE of the mutant embryos, and its forced overexpression mimicked the Wave complex loss-of-function phenotype. Moreover, Wnt signaling, which regulates SOX9+ cell specification, was up-regulated in Wave complex loss-of-function IFE. Importantly, we show that the Wave complex regulates filamentous actin content and that a decrease in actin levels is sufficient to elevate Wnt/β-catenin signaling. Our results identify a novel role for Wave complex– and actin-regulated signaling via Wnt and SOX9 in skin development.
Collapse
Affiliation(s)
- Jonathan Cohen
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shaul Raviv
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orit Adir
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Krishnanand Padmanabhan
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arad Soffer
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Luxenburg
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
17
|
|
18
|
GWAS analysis using interspecific backcross progenies reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish. Mol Genet Genomics 2018; 293:1107-1120. [PMID: 29737402 DOI: 10.1007/s00438-018-1443-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 05/02/2018] [Indexed: 12/11/2022]
Abstract
Infectious diseases pose significant threats to the catfish industry. Enteric septicemia of catfish (ESC) caused by Edwardsiella ictaluri is the most devastating disease for catfish aquaculture, causing huge economic losses annually. Channel catfish and blue catfish exhibit great contrast in resistance against ESC, with channel catfish being highly susceptible and blue catfish being highly resistant. As such, the interspecific backcross progenies provide an ideal system for the identification of quantitative trait locus (QTL). We previously reported one significant QTL on linkage group (LG) 1 using the third-generation backcrosses, but the number of founders used to make the second- and third-generation backcross progenies was very small. Although the third-generation backcross progenies provided a greater power for fine mapping than the first-generation backcrosses, some major QTL for disease resistance may have been missing due to the small numbers of founders used to produce the higher generation backcrosses. In this study, we performed a genome-wide association study using first-generation backcrosses with the catfish 690 K SNP arrays to identify additional ESC disease resistance QTL, especially those at the species level. Two genomic regions on LG1 and LG23 were determined to be significantly associated with ESC resistance as revealed by a mixed linear model and family-based association test. Examination of the resistance alleles indicated their origin from blue catfish, indicating that at least two major disease resistance loci exist among blue catfish populations. Upon further validation, markers linked with major ESC disease resistance QTL should be useful for marker-assisted introgression, allowing development of highly ESC resistant breeds of catfish.
Collapse
|
19
|
Abstract
The molecular composition of the cell wall is critical for the biology and ecology of each fungal species. Fungal walls are composed of matrix components that are embedded and linked to scaffolds of fibrous load-bearing polysaccharides. Most of the major cell wall components of fungal pathogens are not represented in humans, other mammals, or plants, and therefore the immune systems of animals and plants have evolved to recognize many of the conserved elements of fungal walls. For similar reasons the enzymes that assemble fungal cell wall components are excellent targets for antifungal chemotherapies and fungicides. However, for fungal pathogens, the cell wall is often disguised since key signature molecules for immune recognition are sometimes masked by immunologically inert molecules. Cell wall damage leads to the activation of sophisticated fail-safe mechanisms that shore up and repair walls to avoid catastrophic breaching of the integrity of the surface. The frontiers of research on fungal cell walls are moving from a descriptive phase defining the underlying genes and component parts of fungal walls to more dynamic analyses of how the various components are assembled, cross-linked, and modified in response to environmental signals. This review therefore discusses recent advances in research investigating the composition, synthesis, and regulation of cell walls and how the cell wall is targeted by immune recognition systems and the design of antifungal diagnostics and therapeutics.
Collapse
|
20
|
Wu D, Chai Y, Zhu Z, Li W, Ou G, Li W. CED-10-WASP-Arp2/3 signaling axis regulates apoptotic cell corpse engulfment in C. elegans. Dev Biol 2017; 428:215-223. [DOI: 10.1016/j.ydbio.2017.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 01/08/2023]
|
21
|
Abstract
The molecular composition of the cell wall is critical for the biology and ecology of each fungal species. Fungal walls are composed of matrix components that are embedded and linked to scaffolds of fibrous load-bearing polysaccharides. Most of the major cell wall components of fungal pathogens are not represented in humans, other mammals, or plants, and therefore the immune systems of animals and plants have evolved to recognize many of the conserved elements of fungal walls. For similar reasons the enzymes that assemble fungal cell wall components are excellent targets for antifungal chemotherapies and fungicides. However, for fungal pathogens, the cell wall is often disguised since key signature molecules for immune recognition are sometimes masked by immunologically inert molecules. Cell wall damage leads to the activation of sophisticated fail-safe mechanisms that shore up and repair walls to avoid catastrophic breaching of the integrity of the surface. The frontiers of research on fungal cell walls are moving from a descriptive phase defining the underlying genes and component parts of fungal walls to more dynamic analyses of how the various components are assembled, cross-linked, and modified in response to environmental signals. This review therefore discusses recent advances in research investigating the composition, synthesis, and regulation of cell walls and how the cell wall is targeted by immune recognition systems and the design of antifungal diagnostics and therapeutics.
Collapse
Affiliation(s)
- Neil A R Gow
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB252ZD, United Kingdom
| | | | - Carol A Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB252ZD, United Kingdom
| |
Collapse
|
22
|
Peng X, Yan T, Sun M. The WASP-Arp2/3 complex signal cascade is involved in actin-dependent sperm nuclei migration during double fertilization in tobacco and maize. Sci Rep 2017; 7:43161. [PMID: 28225074 PMCID: PMC5320560 DOI: 10.1038/srep43161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/20/2017] [Indexed: 12/14/2022] Open
Abstract
Sperm nuclear migration during fertilization in Arabidopsis and rice has recently been found to be actin-dependent, but the driving force behind this actin cytoskeleton-dependent motion is unclear. Here, we confirmed that the actin-dependent sperm nuclei migration during fertilization is a conserved mechanism in plants. Using in vitro fertilization systems, we showed that a functional actin is also essential in maize and tobacco for sperm nuclei migration after gamete membrane fusion. Cytoskeleton depolymerization inhibitor treatments supported the view that sperm nuclei migration is actin-dependent but microtubule-independent in both egg cell and central cell during double fertilization. We further revealed that the actin-based motor myosin is not the driving force for sperm nuclear migration in maize and tobacco. The WASP-Arp2/3 complex signal cascade is shown here to be involved in the regulation of sperm nuclear migration in maize and tobacco. It is interesting that sperm nuclei migration within somatic cell also need WASP-Arp2/3 complex signal cascade and actin, suggesting that the mechanism of sperm nuclear migration is not gamete specific.
Collapse
Affiliation(s)
- Xiongbo Peng
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tingting Yan
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mengxiang Sun
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| |
Collapse
|
23
|
Qi T, Wang J, Sun Q, Day B, Guo J, Ma Q. TaARPC3, Contributes to Wheat Resistance against the Stripe Rust Fungus. FRONTIERS IN PLANT SCIENCE 2017; 8:1245. [PMID: 28769954 PMCID: PMC5513970 DOI: 10.3389/fpls.2017.01245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/30/2017] [Indexed: 05/19/2023]
Abstract
The actin cytoskeleton participates in numerous cellular processes, including less-characterized processes, such as nuclear organization, chromatin remodeling, transcription, and signal transduction. As a key regulator of actin cytoskeletal dynamics, the actin related protein 2/3 complex (Arp2/3 complex) controls multiple developmental processes in a variety of tissues and cell types. To date, the role of the Arp2/3 complex in plant disease resistance signaling is largely unknown. Herein, we identified and characterized wheat ARPC3, TaARPC3, which encodes the C3 subunit of the Arp2/3 complex. Expression of TaARPC3 in the arc18 mutant of Saccharomyces cerevisiae Δarc18 resulted in complementation of stress-induced phenotypes in S. cerevisiae, as well as restore wild-type cell shape malformations. TaARPC3 was found predominantly to be localized in the nucleus and cytoplasm when expressed transiently in wheat protoplast. TaARPC3 was significantly induced in response to avirulent race of Puccinia striiformis f. sp. tritici (Pst). Knock-down of TaARPC3 by virus-induced gene silencing resulted in a reduction of resistance against Pst through a specific reduction in actin cytoskeletal organization. Interestingly, this reduction was found to coincide with a block in reactive oxygen species (ROS) accumulation, the hypersensitive response (HR), an increase in TaCAT1 mRNA accumulation, and the growth of Pst. Taken together, these findings suggest that TaARPC3 is a key subunit of the Arp2/3 complex which is required for wheat resistance against Pst, a process that is associated with the regulation of the actin cytoskeleton.
Collapse
Affiliation(s)
- Tuo Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Juan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Qixiong Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Brad Day
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East LansingMI, United States
- Plant Resilience Institute, Michigan State University, East LansingMI, United States
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
- *Correspondence: Qing Ma, Jun Guo,
| | - Qing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
- *Correspondence: Qing Ma, Jun Guo,
| |
Collapse
|
24
|
Mu J, Zhang Y, Hu Y, Hu X, Zhou Y, Zhao H, Pei R, Wu C, Chen J, Zhao H, Yang K, van Oers MM, Chen X, Wang Y. Autographa californica Multiple Nucleopolyhedrovirus Ac34 Protein Retains Cellular Actin-Related Protein 2/3 Complex in the Nucleus by Subversion of CRM1-Dependent Nuclear Export. PLoS Pathog 2016; 12:e1005994. [PMID: 27802336 PMCID: PMC5089780 DOI: 10.1371/journal.ppat.1005994] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Actin, nucleation-promoting factors (NPFs), and the actin-related protein 2/3 complex (Arp2/3) are key elements of the cellular actin polymerization machinery. With nuclear actin polymerization implicated in ever-expanding biological processes and the discovery of the nuclear import mechanisms of actin and NPFs, determining Arp2/3 nucleo-cytoplasmic shuttling mechanism is important for understanding the function of nuclear actin. A unique feature of alphabaculovirus infection of insect cells is the robust nuclear accumulation of Arp2/3, which induces actin polymerization in the nucleus to assist in virus replication. We found that Ac34, a viral late gene product encoded by the alphabaculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV), is involved in Arp2/3 nuclear accumulation during virus infection. Further assays revealed that the subcellular distribution of Arp2/3 under steady-state conditions is controlled by chromosomal maintenance 1 (CRM1)-dependent nuclear export. Upon AcMNPV infection, Ac34 inhibits CRM1 pathway and leads to Arp2/3 retention in the nucleus.
Collapse
Affiliation(s)
- Jingfang Mu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongli Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangyang Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yuan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - He Zhao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Rongjuan Pei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Chunchen Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jizheng Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Han Zhao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Yang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, China
| | | | - Xinwen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yun Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
25
|
Coutts AS, La Thangue NB. Regulation of actin nucleation and autophagosome formation. Cell Mol Life Sci 2016; 73:3249-63. [PMID: 27147468 PMCID: PMC4967107 DOI: 10.1007/s00018-016-2224-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/21/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
Abstract
Autophagy is a process of self-eating, whereby cytosolic constituents are enclosed by a double-membrane vesicle before delivery to the lysosome for degradation. This is an important process which allows for recycling of nutrients and cellular components and thus plays a critical role in normal cellular homeostasis as well as cell survival during stresses such as starvation or hypoxia. A large number of proteins regulate various stages of autophagy in a complex and still incompletely understood series of events. In this review, we will discuss recent studies which provide a growing body of evidence that actin dynamics and proteins that influence actin nucleation play an important role in the regulation of autophagosome formation and maturation.
Collapse
Affiliation(s)
- Amanda S Coutts
- Laboratory of Cancer Biology, Medical Sciences Division, Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Off Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Nicholas B La Thangue
- Laboratory of Cancer Biology, Medical Sciences Division, Department of Oncology, University of Oxford, Old Road Campus Research Building, Old Road Campus, Off Roosevelt Drive, Oxford, OX3 7DQ, UK.
| |
Collapse
|
26
|
Zhang HH, Lechuga TJ, Chen Y, Yang Y, Huang L, Chen DB. Quantitative Proteomics Analysis of VEGF-Responsive Endothelial Protein S-Nitrosylation Using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and LC-MS/MS. Biol Reprod 2016; 94:114. [PMID: 27075618 PMCID: PMC4939742 DOI: 10.1095/biolreprod.116.139337] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/08/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022] Open
Abstract
Adduction of a nitric oxide moiety (NO•) to cysteine(s), termed S-nitrosylation (SNO), is a novel mechanism for NO to regulate protein function directly. However, the endothelial SNO-protein network that is affected by endogenous and exogenous NO is obscure. This study was designed to develop a quantitative proteomics approach using stable isotope labeling by amino acids in cell culture for comparing vascular endothelial growth factor (VEGFA)- and NO donor-responsive endothelial nitroso-proteomes. Primary placental endothelial cells were labeled with "light" (L-(12)C6 (14)N4-Arg and L-(12)C6 (14)N2-Lys) or "heavy" (L-(13)C6 (15)N4-Arg and L-(13)C6 (15)N2-Lys) amino acids. The light cells were treated with an NO donor nitrosoglutathione (GSNO, 1 mM) or VEGFA (10 ng/ml) for 30 min, while the heavy cells received vehicle as control. Equal amounts of cellular proteins from the light (GSNO or VEGFA treated) and heavy cells were mixed for labeling SNO-proteins by the biotin switch technique and then trypsin digested. Biotinylated SNO-peptides were purified for identifying SNO-proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Ratios of light to heavy SNO-peptides were calculated for determining the changes of the VEGFA- and GSNO-responsive endothelial nitroso-proteomes. A total of 387 light/heavy pairs of SNO-peptides were identified, corresponding to 213 SNO-proteins that include 125 common and 27 VEGFA- and 61 GSNO-responsive SNO-proteins. The specific SNO-cysteine(s) in each SNO-protein were simultaneously identified. Pathway analysis revealed that SNO-proteins are involved in various endothelial functions, including proliferation, motility, metabolism, and protein synthesis. We collectively conclude that endogenous NO on VEGFA stimulation and exogenous NO from GSNO affect common and different SNO-protein networks, implicating SNO as a critical mechanism for VEGFA stimulation of angiogenesis.
Collapse
Affiliation(s)
- Hong-Hai Zhang
- Department of Obstetrics and Gynecology, University of California, Irvine, California
| | - Thomas J Lechuga
- Department of Obstetrics and Gynecology, University of California, Irvine, California
| | - Yuezhou Chen
- Department of Obstetrics and Gynecology, University of California, Irvine, California
| | - Yingying Yang
- Department of Biophysics and Physiology, University of California, Irvine, California
| | - Lan Huang
- Department of Biophysics and Physiology, University of California, Irvine, California
| | - Dong-Bao Chen
- Department of Obstetrics and Gynecology, University of California, Irvine, California
| |
Collapse
|
27
|
Ravi S, Johnson MS, Chacko BK, Kramer PA, Sawada H, Locy ML, Wilson LS, Barnes S, Marques MB, Darley-Usmar VM. Modification of platelet proteins by 4-hydroxynonenal: Potential Mechanisms for inhibition of aggregation and metabolism. Free Radic Biol Med 2016; 91:143-53. [PMID: 26475426 PMCID: PMC4761519 DOI: 10.1016/j.freeradbiomed.2015.10.408] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/06/2015] [Accepted: 10/10/2015] [Indexed: 01/23/2023]
Abstract
Platelet aggregation is an essential response to tissue injury and is associated with activation of pro-oxidant enzymes, such as cyclooxygenase, and is also a highly energetic process. The two central energetic pathways in the cell, glycolysis and mitochondrial oxidative phosphorylation, are susceptible to damage by reactive lipid species. Interestingly, how platelet metabolism is affected by the oxidative stress associated with aggregation is largely unexplored. To address this issue, we examined the response of human platelets to 4-hydroxynonenal (4-HNE), a reactive lipid species which is generated during thrombus formation and during oxidative stress. Elevated plasma 4-HNE has been associated with renal failure, septic shock and cardiopulmonary bypass surgery. In this study, we found that 4-HNE decreased thrombin stimulated platelet aggregation by approximately 60%. The metabolomics analysis demonstrated that underlying our previous observation of a stimulation of platelet energetics by thrombin glycolysis and TCA (Tricarboxylic acid) metabolites were increased. Next, we assessed the effect of both 4-HNE and alkyne HNE (A-HNE) on bioenergetics and targeted metabolomics, and found a stimulatory effect on glycolysis, associated with inhibition of bioenergetic parameters. In the presence of HNE and thrombin glycolysis was further stimulated but the levels of the TCA metabolites were markedly suppressed. Identification of proteins modified by A-HNE followed by click chemistry and mass spectrometry revealed essential targets in platelet activation including proteins involved in metabolism, adhesion, cytoskeletal reorganization, aggregation, vesicular transport, protein folding, antioxidant proteins, and small GTPases. In summary, the biological effects of 4-HNE can be more effectively explained in platelets by the integrated effects of the modification of an electrophile responsive proteome rather than the isolated effects of candidate proteins.
Collapse
Affiliation(s)
- Saranya Ravi
- Department of Pathology; UAB Mitochondrial Medicine Laboratory; Center for Free Radical Biology
| | - Michelle S Johnson
- Department of Pathology; UAB Mitochondrial Medicine Laboratory; Center for Free Radical Biology
| | - Balu K Chacko
- Department of Pathology; UAB Mitochondrial Medicine Laboratory; Center for Free Radical Biology
| | - Philip A Kramer
- Department of Pathology; UAB Mitochondrial Medicine Laboratory; Center for Free Radical Biology
| | - Hirotaka Sawada
- Department of Pathology; UAB Mitochondrial Medicine Laboratory; Center for Free Radical Biology
| | - Morgan L Locy
- Department of Pathology; UAB Mitochondrial Medicine Laboratory; Center for Free Radical Biology
| | | | - Stephen Barnes
- The Targeted Metabolomics and Proteomics Laboratory; Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Victor M Darley-Usmar
- Department of Pathology; UAB Mitochondrial Medicine Laboratory; Center for Free Radical Biology.
| |
Collapse
|
28
|
Brüser L, Bogdan S. Molecular Control of Actin Dynamics In Vivo: Insights from Drosophila. Handb Exp Pharmacol 2016; 235:285-310. [PMID: 27757759 DOI: 10.1007/164_2016_33] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The actin cytoskeleton provides mechanical support for cells and generates forces to drive cell shape changes and cell migration in morphogenesis. Molecular understanding of actin dynamics requires a genetically traceable model system that allows interdisciplinary experimental approaches to elucidate the regulatory network of cytoskeletal proteins in vivo. Here, we will discuss some examples of how advances in Drosophila genetics and high-resolution imaging techniques contribute to the discovery of new actin functions, signaling pathways, and mechanisms of actin regulation in vivo.
Collapse
Affiliation(s)
- Lena Brüser
- Institute for Neurobiology, University of Muenster, Badestrasse 9, 48149, Muenster, Germany
| | - Sven Bogdan
- Institute for Neurobiology, University of Muenster, Badestrasse 9, 48149, Muenster, Germany.
| |
Collapse
|
29
|
Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy KR, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J. Rapid, optimized interactomic screening. Nat Methods 2015; 12:553-60. [PMID: 25938370 PMCID: PMC4449307 DOI: 10.1038/nmeth.3395] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 03/03/2015] [Indexed: 12/25/2022]
Abstract
We must reliably map the interactomes of cellular macromolecular
complexes in order to fully explore and understand biological systems. However,
there are no methods to accurately predict how to capture a given macromolecular
complex with its physiological binding partners. Here, we present a screen that
comprehensively explores the parameters affecting the stability of interactions
in affinity-captured complexes, enabling the discovery of physiological binding
partners and the elucidation of their functional interactions in unparalleled
detail. We have implemented this screen on several macromolecular complexes from
a variety of organisms, revealing novel profiles even for well-studied proteins.
Our approach is robust, economical and automatable, providing an inroad to the
rigorous, systematic dissection of cellular interactomes.
Collapse
Affiliation(s)
- Zhanna Hakhverdyan
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Michal Domanski
- 1] Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA. [2] Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Loren E Hough
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | | | | | - Sarah Keegan
- 1] Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - David J Dilworth
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Vadim Sherman
- High Energy Physics Instrument Shop, The Rockefeller University, New York, New York, USA
| | - John D Aitchison
- 1] Institute for Systems Biology, Seattle, Washington, USA. [2] Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - David Fenyö
- 1] Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| |
Collapse
|
30
|
Wang Y, Zhang Y, Han S, Hu X, Zhou Y, Mu J, Pei R, Wu C, Chen X. Identification of a novel regulatory sequence of actin nucleation promoting factor encoded by Autographa californica multiple nucleopolyhedrovirus. J Biol Chem 2015; 290:9533-41. [PMID: 25691574 DOI: 10.1074/jbc.m114.635441] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Indexed: 11/06/2022] Open
Abstract
Actin polymerization induced by nucleation promoting factors (NPFs) is one of the most fundamental biological processes in eukaryotic cells. NPFs contain a conserved output domain (VCA domain) near the C terminus, which interacts with and activates the cellular actin-related protein 2/3 complex (Arp2/3) to induce actin polymerization and a diverse regulatory domain near the N terminus. Autographa californica multiple nucleopolyhedrovirus (AcMNPV) nucleocapsid protein P78/83 is a virus-encoded NPF that contains a C-terminal VCA domain and induces actin polymerization in virus-infected cells. However, there is no similarity between the N terminus of P78/83 and that of other identified NPFs, suggesting that P78/83 may possess a unique regulatory mechanism. In this study, we identified a multifunctional regulatory sequence (MRS) located near the N terminus of P78/83 and determined that one of its functions is to serve as a degron to mediate P78/83 degradation in a proteasome-dependent manner. In AcMNPV-infected cells, the MRS also binds to another nucleocapsid protein, BV/ODV-C42, which stabilizes P78/83 and modulates the P78/83-Arp2/3 interaction to orchestrate actin polymerization. In addition, the MRS is also essential for the incorporation of P78/83 into the nucleocapsid, ensuring virion mobility powered by P78/83-induced actin polymerization. The triple functions of the MRS enable P78/83 to serve as an essential viral protein in the AcMNPV replication cycle, and the possible roles of the MRS in orchestrating the virus-induced actin polymerization and viral genome decapsidation are discussed.
Collapse
Affiliation(s)
- Yun Wang
- From the State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 430071,
| | - Yongli Zhang
- From the State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 430071, the University of Chinese Academy of Sciences, Beijing, China, 100049, and
| | - Shili Han
- the Central China Normal University, Wuhan, China, 430000
| | - Xue Hu
- From the State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 430071
| | - Yuan Zhou
- From the State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 430071
| | - Jingfang Mu
- From the State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 430071, the University of Chinese Academy of Sciences, Beijing, China, 100049, and
| | - Rongjuan Pei
- From the State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 430071
| | - Chunchen Wu
- From the State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 430071
| | - Xinwen Chen
- From the State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China, 430071,
| |
Collapse
|
31
|
Applying particle swarm optimization-based decision tree classifier for cancer classification on gene expression data. Appl Soft Comput 2014. [DOI: 10.1016/j.asoc.2014.08.032] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
32
|
Karmakar S, Saha S, Banerjee D, Chakrabarti A. Differential proteomics study of platelets in asymptomatic constitutional macrothrombocytopenia: altered levels of cytoskeletal proteins. Eur J Haematol 2014; 94:43-50. [PMID: 24934967 DOI: 10.1111/ejh.12398] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2014] [Indexed: 12/27/2022]
Abstract
OBJECTIVES Harris platelet syndrome (HPS), also known as asymptomatic constitutional macrothrombocytopenia (ACMT), is an autosomal dominant platelet disorder characterized by mild-to-severe thrombocytopenia and giant platelets with normal platelet aggregation and absence of bleeding symptoms. We have attempted a comparative proteomics study for profiling of platelet proteins in healthy vs. pathological states to discover characteristic protein expression changes in macrothrombocytes and decipher the factors responsible for the functionally active yet morphologically distinct platelets. METHODS We have used 2-D gel-based protein separation techniques coupled with MALDI-ToF/ToF-based mass spectrometric identification and characterization of the proteins to investigate the differential proteome profiling of platelet proteins isolated from the peripheral blood samples of patients and normal volunteers. RESULTS AND CONCLUSION Our study revealed altered levels of actin-binding proteins such as myosin light chain, coactosin-like protein, actin-related protein 2/3 complex, and transgelin2 that hint toward the cytoskeletal changes necessary to maintain the structural and functional integrity of macrothrombocytes. We have also observed over expressed levels of peroxiredoxin2 that signifies the prevailing oxidative stress in these cells. Additionally, altered levels of protein disulfide isomerase and transthyretin provide insights into the measures adapted by the macrothrombocytes to maintain their normal functional activity. This first proteomics study of platelets from ACMT may provide an understanding of the structural stability and normal functioning of these platelets in spite of their large size.
Collapse
Affiliation(s)
- Shilpita Karmakar
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | | | | | | |
Collapse
|
33
|
Yuan B, Wan P, Chu D, Nie J, Cao Y, Luo W, Lu S, Chen J, Yang Z. A cardiomyocyte-specific Wdr1 knockout demonstrates essential functional roles for actin disassembly during myocardial growth and maintenance in mice. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1967-80. [PMID: 24840128 DOI: 10.1016/j.ajpath.2014.04.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 03/26/2014] [Accepted: 04/07/2014] [Indexed: 11/25/2022]
Abstract
Actin dynamics are critical for muscle development and function, and mutations leading to deregulation of actin dynamics cause various forms of heritable muscle diseases. AIP1 is a major cofactor of the actin depolymerizing factor/cofilin in eukaryotes, promoting actin depolymerizing factor/cofilin-mediated actin disassembly. Its function in vertebrate muscle has been unknown. To investigate functional roles of AIP1 in myocardium, we generated conditional knockout (cKO) mice with cardiomyocyte-specific deletion of Wdr1, the mammalian homolog of yeast AIP1. Wdr1 cKO mice began to die at postnatal day 13 (P13), and none survived past P24. At P12, cKO mice exhibited cardiac hypertrophy and impaired contraction of the left ventricle. Electrocardiography revealed reduced heart rate, abnormal P wave, and abnormal T wave at P10 and prolonged QT interval at P12. Actin filament (F-actin) accumulations began at P10 and became prominent at P12 in the myocardium of cKO mice. Within regions of F-actin accumulation in myofibrils, the sarcomeric components α-actinin and tropomodulin-1 exhibited disrupted patterns, indicating that F-actin accumulations caused by Wdr1 deletion result in disruption of sarcomeric structure. Ectopic cofilin colocalized with F-actin aggregates. In adult mice, Wdr1 deletion resulted in similar but much milder phenotypes of heart hypertrophy, F-actin accumulations within myofibrils, and lethality. Taken together, these results demonstrate that AIP1-regulated actin dynamics play essential roles in heart function in mice.
Collapse
Affiliation(s)
- Baiyin Yuan
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Ping Wan
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Dandan Chu
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China; Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
| | - Junwei Nie
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Yunshan Cao
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Wen Luo
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Shuangshuang Lu
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Jiong Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China.
| | - Zhongzhou Yang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
34
|
Hadziselimovic N, Vukojevic V, Peter F, Milnik A, Fastenrath M, Fenyves B, Hieber P, Demougin P, Vogler C, de Quervain DF, Papassotiropoulos A, Stetak A. Forgetting Is Regulated via Musashi-Mediated Translational Control of the Arp2/3 Complex. Cell 2014; 156:1153-1166. [DOI: 10.1016/j.cell.2014.01.054] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 11/27/2013] [Accepted: 01/17/2014] [Indexed: 01/21/2023]
|
35
|
Pavlopoulos GA, Promponas VJ, Ouzounis CA, Iliopoulos I. Biological information extraction and co-occurrence analysis. Methods Mol Biol 2014; 1159:77-92. [PMID: 24788262 DOI: 10.1007/978-1-4939-0709-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Nowadays, it is possible to identify terms corresponding to biological entities within passages in biomedical text corpora: critically, their potential relationships then need to be detected. These relationships are typically detected by co-occurrence analysis, revealing associations between bioentities through their coexistence in single sentences and/or entire abstracts. These associations implicitly define networks, whose nodes represent terms/bioentities/concepts being connected by relationship edges; edge weights might represent confidence for these semantic connections.This chapter provides a review of current methods for co-occurrence analysis, focusing on data storage, analysis, and representation. We highlight scenarios of these approaches implemented by useful tools for information extraction and knowledge inference in the field of systems biology. We illustrate the practical utility of two online resources providing services of this type-namely, STRING and BioTextQuest-concluding with a discussion of current challenges and future perspectives in the field.
Collapse
Affiliation(s)
- Georgios A Pavlopoulos
- Division of Basic Sciences, University of Crete Medical School, Heraklion, 71110, Greece
| | | | | | | |
Collapse
|
36
|
A yeast chemical genetics approach identifies the compound 3,4,5-trimethoxybenzyl isothiocyanate as a calcineurin inhibitor. FEBS Lett 2013; 588:455-8. [DOI: 10.1016/j.febslet.2013.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 11/21/2022]
|
37
|
Ivakov A, Persson S. Plant cell shape: modulators and measurements. FRONTIERS IN PLANT SCIENCE 2013; 4:439. [PMID: 24312104 PMCID: PMC3832843 DOI: 10.3389/fpls.2013.00439] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/14/2013] [Indexed: 05/19/2023]
Abstract
Plant cell shape, seen as an integrative output, is of considerable interest in various fields, such as cell wall research, cytoskeleton dynamics and biomechanics. In this review we summarize the current state of knowledge on cell shape formation in plants focusing on shape of simple cylindrical cells, as well as in complex multipolar cells such as leaf pavement cells and trichomes. We summarize established concepts as well as recent additions to the understanding of how cells construct cell walls of a given shape and the underlying processes. These processes include cell wall synthesis, activity of the actin and microtubule cytoskeletons, in particular their regulation by microtubule associated proteins, actin-related proteins, GTP'ases and their effectors, as well as the recently-elucidated roles of plant hormone signaling and vesicular membrane trafficking. We discuss some of the challenges in cell shape research with a particular emphasis on quantitative imaging and statistical analysis of shape in 2D and 3D, as well as novel developments in this area. Finally, we review recent examples of the use of novel imaging techniques and how they have contributed to our understanding of cell shape formation.
Collapse
Affiliation(s)
- Alexander Ivakov
- *Correspondence: Alexander Ivakov and Staffan Persson, Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany e-mail: ;
| | - Staffan Persson
- *Correspondence: Alexander Ivakov and Staffan Persson, Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany e-mail: ;
| |
Collapse
|
38
|
Zhao Y, Pan Z, Zhang Y, Qu X, Zhang Y, Yang Y, Jiang X, Huang S, Yuan M, Schumaker KS, Guo Y. The actin-related Protein2/3 complex regulates mitochondrial-associated calcium signaling during salt stress in Arabidopsis. THE PLANT CELL 2013; 25:4544-59. [PMID: 24280386 PMCID: PMC3875735 DOI: 10.1105/tpc.113.117887] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/30/2013] [Accepted: 11/14/2013] [Indexed: 05/18/2023]
Abstract
Microfilament and Ca(2+) dynamics play important roles in stress signaling in plants. Through genetic screening of Arabidopsis thaliana mutants that are defective in stress-induced increases in cytosolic Ca(2+) ([Ca(2+)]cyt), we identified Actin-Related Protein2 (Arp2) as a regulator of [Ca(2+)]cyt in response to salt stress. Plants lacking Arp2 or other proteins in the Arp2/3 complex exhibited enhanced salt-induced increases in [Ca(2+)]cyt, decreased mitochondria movement, and hypersensitivity to salt. In addition, mitochondria aggregated, the mitochondrial permeability transition pore opened, and mitochondrial membrane potential Ψm was impaired in the arp2 mutant, and these changes were associated with salt-induced cell death. When opening of the enhanced mitochondrial permeability transition pore was blocked or increases in [Ca(2+)]cyt were prevented, the salt-sensitive phenotype of the arp2 mutant was partially rescued. These results indicate that the Arp2/3 complex regulates mitochondrial-dependent Ca(2+) signaling in response to salt stress.
Collapse
Affiliation(s)
- Yi Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Pan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- College of Life Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaolu Qu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuguo Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yongqing Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiangning Jiang
- College of Life Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- National Engineering Laboratory of Tree Breeding, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of State Forestry Administration, Beijing 100083, China
| | - Shanjin Huang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ming Yuan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | | | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- National Center for Plant Gene Research, Beijing 100193, China
- Address correspondence to
| |
Collapse
|
39
|
Banon-Rodriguez I, Saez de Guinoa J, Bernardini A, Ragazzini C, Fernandez E, Carrasco YR, Jones GE, Wandosell F, Anton IM. WIP regulates persistence of cell migration and ruffle formation in both mesenchymal and amoeboid modes of motility. PLoS One 2013; 8:e70364. [PMID: 23950925 PMCID: PMC3737202 DOI: 10.1371/journal.pone.0070364] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/17/2013] [Indexed: 02/08/2023] Open
Abstract
The spatial distribution of signals downstream from receptor tyrosine kinases (RTKs) or G-protein coupled receptors (GPCR) regulates fundamental cellular processes that control cell migration and growth. Both pathways rely significantly on actin cytoskeleton reorganization mediated by nucleation-promoting factors such as the WASP-(Wiskott-Aldrich Syndrome Protein) family. WIP (WASP Interacting Protein) is essential for the formation of a class of polarised actin microdomain, namely dorsal ruffles, downstream of the RTK for PDGF (platelet-derived growth factor) but the underlying mechanism is poorly understood. Using lentivirally-reconstituted WIP-deficient murine fibroblasts we define the requirement for WIP interaction with N-WASP (neural WASP) and Nck for efficient dorsal ruffle formation and of WIP-Nck binding for fibroblast chemotaxis towards PDGF-AA. The formation of both circular dorsal ruffles in PDGF-AA-stimulated primary fibroblasts and lamellipodia in CXCL13-treated B lymphocytes are also compromised by WIP-deficiency. We provide data to show that a WIP-Nck signalling complex interacts with RTK to promote polarised actin remodelling in fibroblasts and provide the first evidence for WIP involvement in the control of migratory persistence in both mesenchymal (fibroblast) and amoeboid (B lymphocytes) motility.
Collapse
Affiliation(s)
| | - Julia Saez de Guinoa
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Alejandra Bernardini
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Chiara Ragazzini
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Estefania Fernandez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Yolanda R. Carrasco
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gareth E. Jones
- The Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Francisco Wandosell
- Department of Molecular Neurobiology, Centro de Biología Molecular “Severo Ochoa” (CBM-UAM), Madrid, Spain
| | - Ines Maria Anton
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- * E-mail:
| |
Collapse
|
40
|
Chaki SP, Rivera GM. Integration of signaling and cytoskeletal remodeling by Nck in directional cell migration. BIOARCHITECTURE 2013; 3:57-63. [PMID: 23887203 PMCID: PMC3782540 DOI: 10.4161/bioa.25744] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Planar and apical-basal cellular polarization of epithelia and endothelia are crucial during morphogenesis. The establishment of these distinct polarity states and their transitions are regulated by signaling networks that include polarity complexes, Rho GTPases, and phosphoinositides. The spatiotemporal coordination of signaling by these molecules modulates cytoskeletal remodeling and vesicle trafficking to specify membrane domains, a prerequisite for the organization of tissues and organs. Here we present an overview of how activation of the WASp/Arp2/3 pathway of actin remodeling by Nck coordinates directional cell migration and speculate on its role as a signaling integrator in the coordination of cellular processes involved in endothelial cell polarity and vascular lumen formation.
Collapse
Affiliation(s)
- Sankar P Chaki
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, USA
| | | |
Collapse
|
41
|
Insight into actin organization and function in cytokinesis from analysis of fission yeast mutants. Genetics 2013; 194:435-46. [PMID: 23589458 DOI: 10.1534/genetics.113.149716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Actin is a key cytoskeletal protein with multiple roles in cellular processes such as polarized growth, cytokinesis, endocytosis, and cell migration. Actin is present in all eukaryotes as highly dynamic filamentous structures, such as linear cables and branched filaments. Detailed investigation of the molecular role of actin in various processes has been hampered due to the multifunctionality of the protein and the lack of alleles defective in specific processes. The actin cytoskeleton of the fission yeast, Schizosaccharomyces pombe, has been extensively characterized and contains structures analogous to those in other cell types. In this study, primarily with the view to uncover actin function in cytokinesis, we generated a large bank of fission yeast actin mutants that affect the organization of distinct actin structures and/or discrete physiological functions of actin. Our screen identified 17 mutants with specific defects in cytokinesis. Some of these cytokinesis mutants helped in dissecting the function of specific actin structures during ring assembly. Further genetic analysis of some of these actin mutants revealed multiple genetic interactions with mutants previously known to affect the actomyosin ring assembly. We also characterize a mutant allele of actin that is suppressed upon overexpression of Cdc8p-tropomyosin, underscoring the utility of this mutant bank. Another 22 mutant alleles, defective in polarized growth and/or other functions of actin obtained from this screen, are also described in this article. This mutant bank should be a valuable resource to study the physiological and biochemical functions of actin.
Collapse
|
42
|
Oda A, Eto K. WASPs and WAVEs: from molecular function to physiology in hematopoietic cells. Semin Cell Dev Biol 2013; 24:308-13. [PMID: 23499790 DOI: 10.1016/j.semcdb.2013.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 03/04/2013] [Indexed: 12/29/2022]
Abstract
The actin cytoskeleton is critically involved in a variety of cell functions. The Arp2/3 complex mediates branching of filamentous actin. The members of the Wiskott-Aldrich syndrome protein (WASP) family are major regulators of the complex. As such, the family proteins are also involved in numerous aspects of cell biology. In this short review, we first define the expanding WASP family. Next, we compare the domain structure of the members, and explain the known or proposed functions of each domain or region. Finally, we demonstrate the well-characterized roles of the proteins in specific cellular functions.
Collapse
Affiliation(s)
- Atsushi Oda
- Department of Internal Medicine, Noguchi Hospital, Ashibetsu 075-0002, Japan.
| | | |
Collapse
|
43
|
|
44
|
Liu J, Wang QC, Wang F, Duan X, Dai XX, Wang T, Liu HL, Cui XS, Kim NH, Sun SC. Nucleation promoting factors regulate the expression and localization of Arp2/3 complex during meiosis of mouse oocytes. PLoS One 2012; 7:e52277. [PMID: 23272233 PMCID: PMC3525642 DOI: 10.1371/journal.pone.0052277] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/12/2012] [Indexed: 11/18/2022] Open
Abstract
The actin nucleation factor Arp2/3 complex is a main regulator of actin assembly and is involved in multiple processes like cell migration and adhesion, endocytosis, and the establishment of cell polarity in mitosis. Our previous work showed that the Arp2/3 complex was involved in the actin-mediated mammalian oocyte asymmetric division. However, the regulatory mechanisms and signaling pathway of Arp2/3 complex in meiosis is still unclear. In the present work, we identified that the nucleation promoting factors (NPFs) JMY and WAVE2 were necessary for the expression and localization of Arp2/3 complex in mouse oocytes. RNAi of both caused the degradation of actin cap intensity, indicating the roles of NPFs in the formation of actin cap. Moreover, JMY and WAVE2 RNAi decreased the expression of ARP2, a key component of Arp2/3 complex. However, knock down of Arp2/3 complex by Arpc2 and Arpc3 siRNA microinjection did not affect the expression and localization of JMY and WAVE2. Our results indicate that the NPFs, JMY and WAVE2, are upstream regulators of Arp2/3 complex in mammalian oocyte asymmetric division.
Collapse
Affiliation(s)
- Jun Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qiao-Chu Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fei Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xing Duan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Xin Dai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Teng Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hong-Lin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiang-Shun Cui
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungbuk, Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju, Chungbuk, Korea
| | - Shao-Chen Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- * E-mail:
| |
Collapse
|
45
|
Lee ST, Wu YL, Chien LH, Chen ST, Tzeng YK, Wu TF. Proteomic exploration of the impacts of pomegranate fruit juice on the global gene expression of prostate cancer cell. Proteomics 2012; 12:3251-62. [DOI: 10.1002/pmic.201200084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 07/12/2012] [Accepted: 08/14/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Song-Tay Lee
- Department of Biotechnology; Southern Taiwan University of Science and Technology; Tainan Taiwan
| | - Yi-Ling Wu
- Department of Biotechnology; Southern Taiwan University of Science and Technology; Tainan Taiwan
| | - Lan-Hsiang Chien
- Department of Biotechnology; Southern Taiwan University of Science and Technology; Tainan Taiwan
| | - Szu-Ting Chen
- Department of Biotechnology; Southern Taiwan University of Science and Technology; Tainan Taiwan
| | - Yu-Kai Tzeng
- Department of Biotechnology; Southern Taiwan University of Science and Technology; Tainan Taiwan
| | - Ting-Feng Wu
- Department of Biotechnology; Southern Taiwan University of Science and Technology; Tainan Taiwan
| |
Collapse
|
46
|
Wang Y, Grainger DW. RNA therapeutics targeting osteoclast-mediated excessive bone resorption. Adv Drug Deliv Rev 2012; 64:1341-57. [PMID: 21945356 DOI: 10.1016/j.addr.2011.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 09/05/2011] [Indexed: 01/13/2023]
Abstract
RNA interference (RNAi) is a sequence-specific post-transcriptional gene silencing technique developed with dramatically increasing utility for both scientific and therapeutic purposes. Short interfering RNA (siRNA) is currently exploited to regulate protein expression relevant to many therapeutic applications, and commonly used as a tool for elucidating disease-associated genes. Osteoporosis and their associated osteoporotic fragility fractures in both men and women are rapidly becoming a global healthcare crisis as average life expectancy increases worldwide. New therapeutics are needed for this increasing patient population. This review describes the diversity of molecular targets suitable for RNAi-based gene knock down in osteoclasts to control osteoclast-mediated excessive bone resorption. We identify strategies for developing targeted siRNA delivery and efficient gene silencing, and describe opportunities and challenges of introducing siRNA as a therapeutic approach to hard and connective tissue disorders.
Collapse
|
47
|
Catucci M, Castiello MC, Pala F, Bosticardo M, Villa A. Autoimmunity in wiskott-Aldrich syndrome: an unsolved enigma. Front Immunol 2012; 3:209. [PMID: 22826711 PMCID: PMC3399097 DOI: 10.3389/fimmu.2012.00209] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/01/2012] [Indexed: 12/17/2022] Open
Abstract
Wiskott-Aldrich Syndrome (WAS) is a severe X-linked Primary Immunodeficiency that affects 1-10 out of 1 million male individuals. WAS is caused by mutations in the WAS Protein (WASP) expressing gene that leads to the absent or reduced expression of the protein. WASP is a cytoplasmic protein that regulates the formation of actin filaments in hematopoietic cells. WASP deficiency causes many immune cell defects both in humans and in the WAS murine model, the Was(-/-) mouse. Both cellular and humoral immune defects in WAS patients contribute to the onset of severe clinical manifestations, in particular microthrombocytopenia, eczema, recurrent infections, and a high susceptibility to develop autoimmunity and malignancies. Autoimmune diseases affect from 22 to 72% of WAS patients and the most common manifestation is autoimmune hemolytic anemia, followed by vasculitis, arthritis, neutropenia, inflammatory bowel disease, and IgA nephropathy. Many groups have widely explored immune cell functionality in WAS partially explaining how cellular defects may lead to pathology. However, the mechanisms underlying the occurrence of autoimmune manifestations have not been clearly described yet. In the present review, we report the most recent progresses in the study of immune cell function in WAS that have started to unveil the mechanisms contributing to autoimmune complications in WAS patients.
Collapse
Affiliation(s)
- Marco Catucci
- San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET) Milan, Italy
| | | | | | | | | |
Collapse
|
48
|
Tang VW, Brieher WM. α-Actinin-4/FSGS1 is required for Arp2/3-dependent actin assembly at the adherens junction. ACTA ACUST UNITED AC 2012; 196:115-30. [PMID: 22232703 PMCID: PMC3255975 DOI: 10.1083/jcb.201103116] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have developed an in vitro assay to study actin assembly at cadherin-enriched cell junctions. Using this assay, we demonstrate that cadherin-enriched junctions can polymerize new actin filaments but cannot capture preexisting filaments, suggesting a mechanism involving de novo synthesis. In agreement with this hypothesis, inhibition of Arp2/3-dependent nucleation abolished actin assembly at cell-cell junctions. Reconstitution biochemistry using the in vitro actin assembly assay identified α-actinin-4/focal segmental glomerulosclerosis 1 (FSGS1) as an essential factor. α-Actinin-4 specifically localized to sites of actin incorporation on purified membranes and at apical junctions in Madin-Darby canine kidney cells. Knockdown of α-actinin-4 decreased total junctional actin and inhibited actin assembly at the apical junction. Furthermore, a point mutation of α-actinin-4 (K255E) associated with FSGS failed to support actin assembly and acted as a dominant negative to disrupt actin dynamics at junctional complexes. These findings demonstrate that α-actinin-4 plays an important role in coupling actin nucleation to assembly at cadherin-based cell-cell adhesive contacts.
Collapse
Affiliation(s)
- Vivian W Tang
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA
| | | |
Collapse
|
49
|
Ziegler ME, Souda P, Jin YP, Whitelegge JP, Reed EF. Characterization of the endothelial cell cytoskeleton following HLA class I ligation. PLoS One 2012; 7:e29472. [PMID: 22247778 PMCID: PMC3256144 DOI: 10.1371/journal.pone.0029472] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 11/29/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Vascular endothelial cells (ECs) are a target of antibody-mediated allograft rejection. In vitro, when the HLA class I molecules on the surface of ECs are ligated by anti-HLA class I antibodies, cell proliferation and survival pathways are activated and this is thought to contribute to the development of antibody-mediated rejection. Crosslinking of HLA class I molecules by anti-HLA antibodies also triggers reorganization of the cytoskeleton, which induces the formation of F-actin stress fibers. HLA class I induced stress fiber formation is not well understood. METHODOLOGY AND PRINCIPAL FINDINGS The present study examines the protein composition of the cytoskeleton fraction of ECs treated with HLA class I antibodies and compares it to other agonists known to induce alterations of the cytoskeleton in endothelial cells. Analysis by tandem mass spectrometry revealed unique cytoskeleton proteomes for each treatment group. Using annotation tools a candidate list was created that revealed 12 proteins, which were unique to the HLA class I stimulated group. Eleven of the candidate proteins were phosphoproteins and exploration of their predicted kinases provided clues as to how these proteins may contribute to the understanding of HLA class I induced antibody-mediated rejection. Three of the candidates, eukaryotic initiation factor 4A1 (eIF4A1), Tropomyosin alpha 4-chain (TPM4) and DDX3X, were further characterized by Western blot and found to be associated with the cytoskeleton. Confocal microscopy analysis showed that class I ligation stimulated increased eIF4A1 co-localization with F-actin and paxillin. CONCLUSIONS/SIGNIFICANCE Colocalization of eIF4A1 with F-actin and paxillin following HLA class I ligation suggests that this candidate protein could be a target for understanding the mechanism(s) of class I mediated antibody-mediated rejection. This proteomic approach for analyzing the cytoskeleton of ECs can be applied to other agonists and various cells types as a method for uncovering novel regulators of cytoskeleton changes.
Collapse
Affiliation(s)
- Mary E. Ziegler
- The Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Puneet Souda
- The Pasarow Mass Spectrometry Laboratory, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yi-Ping Jin
- The Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Elaine F. Reed
- The Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
50
|
A transcriptional program promotes remodeling of GABAergic synapses in Caenorhabditis elegans. J Neurosci 2011; 31:15362-75. [PMID: 22031882 DOI: 10.1523/jneurosci.3181-11.2011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Although transcription factors are known to regulate synaptic plasticity, downstream genes that contribute to neural circuit remodeling are largely undefined. In Caenorhabditis elegans, GABAergic Dorsal D (DD) motor neuron synapses are relocated to new sites during larval development. This remodeling program is blocked in Ventral D (VD) GABAergic motor neurons by the COUP-TF (chicken ovalbumin upstream promoter transcription factor) homolog, UNC-55. We exploited this UNC-55 function to identify downstream synaptic remodeling genes that encode a diverse array of protein types including ion channels, cytoskeletal components, and transcription factors. We show that one of these targets, the Iroquois-like homeodomain protein, IRX-1, functions as a key regulator of remodeling in DD neurons. Our discovery of irx-1 as an unc-55-regulated target defines a transcriptional pathway that orchestrates an intricate synaptic remodeling program. Moreover, the well established roles of these conserved transcription factors in mammalian neural development suggest that a similar cascade may also control synaptic plasticity in more complex nervous systems.
Collapse
|