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Li CLF, Santhanam B, Webb AN, Zupan B, Shaulsky G. Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium. Genome Res 2016; 26:1268-76. [PMID: 27307293 PMCID: PMC5052037 DOI: 10.1101/gr.205682.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/17/2016] [Indexed: 11/24/2022]
Abstract
Whole-genome sequencing is a useful approach for identification of chemical-induced lesions, but previous applications involved tedious genetic mapping to pinpoint the causative mutations. We propose that saturation mutagenesis under low mutagenic loads, followed by whole-genome sequencing, should allow direct implication of genes by identifying multiple independent alleles of each relevant gene. We tested the hypothesis by performing three genetic screens with chemical mutagenesis in the social soil amoeba Dictyostelium discoideum Through genome sequencing, we successfully identified mutant genes with multiple alleles in near-saturation screens, including resistance to intense illumination and strong suppressors of defects in an allorecognition pathway. We tested the causality of the mutations by comparison to published data and by direct complementation tests, finding both dominant and recessive causative mutations. Therefore, our strategy provides a cost- and time-efficient approach to gene discovery by integrating chemical mutagenesis and whole-genome sequencing. The method should be applicable to many microbial systems, and it is expected to revolutionize the field of functional genomics in Dictyostelium by greatly expanding the mutation spectrum relative to other common mutagenesis methods.
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Affiliation(s)
- Cheng-Lin Frank Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Balaji Santhanam
- Graduate Program in Structural Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amanda Nicole Webb
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Blaž Zupan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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52
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Varnaitė R, MacNeill SA. Meet the neighbors: Mapping local protein interactomes by proximity-dependent labeling with BioID. Proteomics 2016; 16:2503-2518. [PMID: 27329485 PMCID: PMC5053326 DOI: 10.1002/pmic.201600123] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/23/2016] [Accepted: 06/16/2016] [Indexed: 12/13/2022]
Abstract
Proximity-dependent biotin identification (BioID) is a recently developed method that allows the identification of proteins in the close vicinity of a protein of interest in living cells. BioID relies on fusion of the protein of interest with a mutant form of the biotin ligase enzyme BirA (BirA*) that is capable of promiscuously biotinylating proximal proteins irrespective of whether these interact directly or indirectly with the fusion protein or are merely located in the same subcellular neighborhood. The covalent addition of biotin allows the labeled proteins to be purified from cell extracts on the basis of their affinity for streptavidin and identified by mass spectrometry. To date, BioID has been successfully applied to study a variety of proteins and processes in mammalian cells and unicellular eukaryotes and has been shown to be particularly suited to the study of insoluble or inaccessible cellular structures and for detecting weak or transient protein associations. Here, we provide an introduction to BioID, together with a detailed summary of where and how the method has been applied to date, and briefly discuss technical aspects involved in the planning and execution of a BioID study.
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Affiliation(s)
- Renata Varnaitė
- School of Biology, University of St Andrews, North Haugh, St Andrews, Scotland, UK
| | - Stuart A MacNeill
- School of Biology, University of St Andrews, North Haugh, St Andrews, Scotland, UK.
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53
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Woods LC, Berbusse GW, Naylor K. Microtubules Are Essential for Mitochondrial Dynamics-Fission, Fusion, and Motility-in Dictyostelium discoideum. Front Cell Dev Biol 2016; 4:19. [PMID: 27047941 PMCID: PMC4801864 DOI: 10.3389/fcell.2016.00019] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/03/2016] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial function is dependent upon mitochondrial structure which is in turn dependent upon mitochondrial dynamics, including fission, fusion, and motility. Here we examined the relationship between mitochondrial dynamics and the cytoskeleton in Dictyostelium discoideum. Using time-lapse analysis, we quantified mitochondrial fission, fusion, and motility in the presence of cytoskeleton disrupting pharmaceuticals and the absence of the potential mitochondria-cytoskeleton linker protein, CluA. Our results indicate that microtubules are essential for mitochondrial movement, as well as fission and fusion; actin plays a less significant role, perhaps selecting the mitochondria for transport. We also suggest that CluA is not a linker protein but plays an unidentified role in mitochondrial fission and fusion. The significance of our work is to gain further insight into the role the cytoskeleton plays in mitochondrial dynamics and function. By better understanding these processes we can better appreciate the underlying mitochondrial contributions to many neurological disorders characterized by altered mitochondrial dynamics, structure, and/or function.
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Affiliation(s)
- Laken C. Woods
- Department of Biology, University of Central ArkansasConway, AR, USA
| | - Gregory W. Berbusse
- Interdisciplinary Biomedical Sciences, University of Arkansas for Medical SciencesLittle Rock, AR, USA
| | - Kari Naylor
- Department of Biology, University of Central ArkansasConway, AR, USA
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54
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Eder M, Koch M, Muth C, Rutz A, Weiss IM. In vivo modified organic matrix for testing biomineralization-related protein functions in differentiated Dictyostelium on calcite. J Struct Biol 2016; 196:85-97. [PMID: 26993464 DOI: 10.1016/j.jsb.2016.03.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 02/29/2016] [Accepted: 03/15/2016] [Indexed: 11/17/2022]
Abstract
This work reports an in vivo approach for identifying the function of biomineralization-related proteins. Synthetic sequences of n16N, OC-17 and perlucin with signal peptides are produced in a novel Gateway expression system for Dictyostelium under the control of the [ecmB] promoter. A fast and easy scanning electron microscopic screening method was used to differentiate on the colony level between interplay effects of the proteins expressed in the extracellular matrix (ECM). Transformed Dictyostelium, which migrated as multicellular colonies on calcite crystals and left their ECM remnants on the surface were investigated also by energy-dispersive X-ray spectroscopy (EDX). Calcium minerals with and without phosphorous accumulated very frequently within the matrix of the Dictyostelium colonies when grown on calcite. Magnesium containing phosphorous granules were observed when colonies were exposed on silica. The absence of calcium EDX signals in these cases suggests that the external calcite crystals but not living cells represent the major source of calcium in the ECM. Several features of the system provide first evidence that each protein influences the properties of the matrix in a characteristic mode. Colonies transformed with perlucin produced a matrix with cracks on the length scale of a few microns throughout the matrix patch. For colonies with OC-17, almost no cracks were observed, regardless of the length scale. The non-transformed Dictyostelium (Ax3-Orf+) produced larger cracks. The strategy presented here develops the first step toward an efficient eukaryotic screening system for the combinatorial functionalization of materials by bioengineering in close analogy to natural biomineralization concepts.
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Affiliation(s)
- Magdalena Eder
- INM - Leibniz Institute for New Materials, Campus D2.2, 66123 Saarbrücken, Germany
| | - Marcus Koch
- INM - Leibniz Institute for New Materials, Campus D2.2, 66123 Saarbrücken, Germany
| | - Christina Muth
- INM - Leibniz Institute for New Materials, Campus D2.2, 66123 Saarbrücken, Germany
| | - Angela Rutz
- INM - Leibniz Institute for New Materials, Campus D2.2, 66123 Saarbrücken, Germany
| | - Ingrid M Weiss
- INM - Leibniz Institute for New Materials, Campus D2.2, 66123 Saarbrücken, Germany.
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55
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Xiong Q, Ünal C, Matthias J, Steinert M, Eichinger L. The phenotypes of ATG9, ATG16 and ATG9/16 knock-out mutants imply autophagy-dependent and -independent functions. Open Biol 2016; 5:150008. [PMID: 25878144 PMCID: PMC4422124 DOI: 10.1098/rsob.150008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Macroautophagy is a highly conserved intracellular bulk degradation system of all eukaryotic cells. It is governed by a large number of autophagy proteins (ATGs) and is crucial for many cellular processes. Here, we describe the phenotypes of Dictyostelium discoideum ATG16(-) and ATG9(-)/16(-) cells and compare them to the previously reported ATG9(-) mutant. ATG16 deficiency caused an increase in the expression of several core autophagy genes, among them atg9 and the two atg8 paralogues. The single and double ATG9 and ATG16 knock-out mutants had complex phenotypes and displayed severe and comparable defects in pinocytosis and phagocytosis. Uptake of Legionella pneumophila was reduced. In addition, ATG9(-) and ATG16(-) cells had dramatic defects in autophagy, development and proteasomal activity which were much more severe in the ATG9(-)/16(-) double mutant. Mutant cells showed an increase in poly-ubiquitinated proteins and contained large ubiquitin-positive protein aggregates which partially co-localized with ATG16-GFP in ATG9(-)/16(-) cells. The more severe autophagic, developmental and proteasomal phenotypes of ATG9(-)/16(-) cells imply that ATG9 and ATG16 probably function in parallel in autophagy and have in addition autophagy-independent functions in further cellular processes.
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Affiliation(s)
- Qiuhong Xiong
- Zentrum für Biochemie, Medizinische Fakultät, Universität zu Köln, Joseph-Stelzmann-Strasse 52, Köln 50931, Germany
| | - Can Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, Braunschweig 38106, Germany Fen Fakültesi, Türk-Alman-Üniversitesi, Istanbul 34820, Turkey
| | - Jan Matthias
- Zentrum für Biochemie, Medizinische Fakultät, Universität zu Köln, Joseph-Stelzmann-Strasse 52, Köln 50931, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, Braunschweig 38106, Germany Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Ludwig Eichinger
- Zentrum für Biochemie, Medizinische Fakultät, Universität zu Köln, Joseph-Stelzmann-Strasse 52, Köln 50931, Germany
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Wessels DJ, Lusche DF, Kuhl S, Scherer A, Voss E, Soll DR. Quantitative Motion Analysis in Two and Three Dimensions. Methods Mol Biol 2016; 1365:265-92. [PMID: 26498790 DOI: 10.1007/978-1-4939-3124-8_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This chapter describes 2D quantitative methods for motion analysis as well as 3D motion analysis and reconstruction methods. Emphasis is placed on the analysis of dynamic cell shape changes that occur through extension and retraction of force generating structures such as pseudopodia and lamellipodia. Quantitative analysis of these structures is an underutilized tool in the field of cell migration. Our intent, therefore, is to present methods that we developed in an effort to elucidate mechanisms of basic cell motility, directed cell motion during chemotaxis, and metastasis. We hope to demonstrate how application of these methods can more clearly define alterations in motility that arise due to specific mutations or disease and hence, suggest mechanisms or pathways involved in normal cell crawling and treatment strategies in the case of disease. In addition, we present a 4D tumorigenesis model for high-resolution analysis of cancer cells from cell lines and human cancer tissue in a 3D matrix. Use of this model led to the discovery of the coalescence of cancer cell aggregates and unique cell behaviors not seen in normal cells or normal tissue. Graphic illustrations to visually display and quantify cell shape are presented along with algorithms and formulae for calculating select 2D and 3D motion analysis parameters.
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Affiliation(s)
- Deborah J Wessels
- W.M. Keck Dynamic Image Analysis Facility, Department of Biological Sciences, University of Iowa, 302 BBE, Iowa City, IA, 52242, USA
| | - Daniel F Lusche
- W.M. Keck Dynamic Image Analysis Facility, Department of Biological Sciences, University of Iowa, 302 BBE, Iowa City, IA, 52242, USA
| | - Spencer Kuhl
- W.M. Keck Dynamic Image Analysis Facility, Department of Biological Sciences, University of Iowa, 302 BBE, Iowa City, IA, 52242, USA
| | - Amanda Scherer
- W.M. Keck Dynamic Image Analysis Facility, Department of Biological Sciences, University of Iowa, 302 BBE, Iowa City, IA, 52242, USA
| | - Edward Voss
- W.M. Keck Dynamic Image Analysis Facility, Department of Biological Sciences, University of Iowa, 302 BBE, Iowa City, IA, 52242, USA
| | - David R Soll
- W.M. Keck Dynamic Image Analysis Facility, Department of Biological Sciences, University of Iowa, 302 BBE, Iowa City, IA, 52242, USA.
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57
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Takács-Vellai K, Vellai T, Farkas Z, Mehta A. Nucleoside diphosphate kinases (NDPKs) in animal development. Cell Mol Life Sci 2015; 72:1447-62. [PMID: 25537302 PMCID: PMC11113130 DOI: 10.1007/s00018-014-1803-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 12/25/2022]
Abstract
In textbooks of biochemistry, nucleoside diphosphate conversion to a triphosphate by nucleoside diphosphate 'kinases' (NDPKs, also named NME or NM23 proteins) merits a few lines of text. Yet this essential metabolic function, mediated by a multimeric phosphotransferase protein, has effects that lie beyond a simple housekeeping role. NDPKs attracted more attention when NM23-H1 was identified as the first metastasis suppressor gene. In this review, we examine these NDPK enzymes from a developmental perspective because of the tractable phenotypes found in simple animal models that point to common themes. The data suggest that NDPK enzymes control the availability of surface receptors to regulate cell-sensing cues during cell migration. NDPKs regulate different forms of membrane enclosure that engulf dying cells during development. We suggest that NDPK enzymes have been essential for the regulated uptake of objects such as bacteria or micronutrients, and this evolutionarily conserved endocytic function contributes to their activity towards the regulation of metastasis.
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Affiliation(s)
- Krisztina Takács-Vellai
- Department of Biological Anthropology, Eötvös Loránd University, Pázmány Péter stny. 1/C, 1117, Budapest, Hungary,
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58
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Priebe M, Bernhardt M, Blum C, Tarantola M, Bodenschatz E, Salditt T. Scanning x-ray nanodiffraction on Dictyostelium discoideum. Biophys J 2014; 107:2662-73. [PMID: 25468345 PMCID: PMC4255453 DOI: 10.1016/j.bpj.2014.10.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/30/2014] [Accepted: 10/14/2014] [Indexed: 12/22/2022] Open
Abstract
We have performed scanning x-ray nanobeam diffraction experiments on single cells of the amoeba Dictyostelium discoideum. Cells have been investigated in 1), freeze-dried, 2), frozen-hydrated (vitrified), and 3), initially alive states. The spatially resolved small-angle x-ray scattering signal shows characteristic streaklike patterns in reciprocal space, which we attribute to fiber bundles of the actomyosin network. From the intensity distributions, an anisotropy parameter can be derived that indicates pronounced local variations within the cell. In addition to nanobeam small-angle x-ray scattering, we have evaluated the x-ray differential phase contrast in view of the projected electron density. Different experimental aspects of the x-ray experiment, sample preparation, and data analysis are discussed. Finally, the x-ray results are correlated with optical microscopy (differential phase contrast and confocal microscopy of mutant strains with fluorescently labeled actin and myosin II), which have been carried out in live and fixed states, including optical microscopy under cryogenic conditions.
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Affiliation(s)
- Marius Priebe
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Marten Bernhardt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Christoph Blum
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Marco Tarantola
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | | | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Göttingen, Germany.
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59
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Gerhardt M, Walz M, Beta C. Signaling in chemotactic amoebae remains spatially confined to stimulated membrane regions. J Cell Sci 2014; 127:5115-25. [PMID: 25300796 DOI: 10.1242/jcs.161133] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recent work has demonstrated that the receptor-mediated signaling system in chemotactic amoeboid cells shows typical properties of an excitable system. Here, we delivered spatially confined stimuli of the chemoattractant cAMP to the membrane of differentiated Dictyostelium discoideum cells to investigate whether localized receptor stimuli can induce the spreading of excitable waves in the G-protein-dependent signal transduction system. By imaging the spatiotemporal dynamics of fluorescent markers for phosphatidylinositol (3,4,5)-trisphosphate (PIP₃), PTEN and filamentous actin, we observed that the activity of the signaling pathway remained spatially confined to the stimulated membrane region. Neighboring parts of the membrane were not excited and no receptor-initiated spatial spreading of excitation waves was observed. To generate localized cAMP stimuli, either particles that carried covalently bound cAMP molecules on their surface were brought into contact with the cell or a patch of the cell membrane was aspirated into a glass micropipette to shield this patch against freely diffusing cAMP molecules in the surrounding medium. Additionally, the binding site of the cAMP receptor was probed with different surface-immobilized cAMP molecules, confirming results from earlier ligand-binding studies.
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Affiliation(s)
- Matthias Gerhardt
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany
| | - Michael Walz
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Strasse 24/25, 14476 Potsdam, Germany
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60
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Vorotnikov AV, Tyurin-Kuzmin PA. Chemotactic signaling in mesenchymal cells compared to amoeboid cells. Genes Dis 2014; 1:162-173. [PMID: 30258862 PMCID: PMC6150068 DOI: 10.1016/j.gendis.2014.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/15/2014] [Indexed: 01/09/2023] Open
Abstract
Cell chemotaxis plays a pivotal role in normal development, inflammatory response, injury repair and tissue regeneration in all organisms. It is also a critical contributor to cancer metastasis, altered angiogenesis and neurite growth in disease. The molecular mechanisms regulating chemotaxis are currently being identified and key components may be pertinent therapeutic targets. Although these components appear to be mostly common in various cells, there are important differences in chemotactic signaling networks and signal processing that result in the distinct chemotactic behavior of mesenchymal cells compared to much better studied amoeboid blood cells. These differences are not necessarily predetermined based on cell type, but are rather chosen and exploited by cells to modify their chemotactic behavior based on physical constraints and/or environmental conditions. This results in a specific type of chemotactic migration in mesenchymal cells that can be selectively targeted in disease. Here, we compare the chemotactic behavior, signaling and motility of mesenchymal and amoeboid cells. We suggest that the current model of chemotaxis is applicable for small amoeboid cells but needs to be reconsidered for large mesenchymal cells. We focus on new candidate regulatory molecules and feedback mechanisms that may account for mesenchymal cell type-specific chemotaxis.
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Key Words
- Chemotaxis
- Feedback regulation
- Fibroblasts
- GEFs, guanine nucleotide exchange factors
- GPCRs, G-protein coupled receptors
- Hydrogen peroxide
- LEGI, local excitation and global inhibition
- MAP-kinase, mitogen-activated protein kinase
- NOX, NADPH-oxidase
- PDGF, platelet derived growth factor
- PI3-kinase, phosphatidylinositol-3-kinase
- PIP3, phosphatidylinositol (3,4,5)-trisphosphate
- PLA2, phospholipase A2
- PTEN, phosphatase and tensin homolog
- RTKs, receptor tyrosine kinases
- Signaling
- mTORC, mechanistic target of rapamycin complex
- РТР-1В, protein tyrosine phosphatase-1B
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Affiliation(s)
- Alexander V. Vorotnikov
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
- Institute of Experimental Cardiology, Russian Cardiology Research and Production Complex, Moscow, Russian Federation
- Corresponding author. Department of Biochemistry and Molecular Medicine, Faculty of Fundamental Medicine, Moscow State University, 31 Lomonosov Ave., Bldg 5, Russian Federation.
| | - Pyotr A. Tyurin-Kuzmin
- Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
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Lusche DF, Wessels D, Richardson NA, Russell KB, Hanson BM, Soll BA, Lin BH, Soll DR. PTEN redundancy: overexpressing lpten, a homolog of Dictyostelium discoideum ptenA, the ortholog of human PTEN, rescues all behavioral defects of the mutant ptenA-. PLoS One 2014; 9:e108495. [PMID: 25247494 PMCID: PMC4172592 DOI: 10.1371/journal.pone.0108495] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/22/2014] [Indexed: 11/18/2022] Open
Abstract
Mutations in the tumor suppressor gene PTEN are associated with a significant proportion of human cancers. Because the human genome also contains several homologs of PTEN, we considered the hypothesis that if a homolog, functionally redundant with PTEN, can be overexpressed, it may rescue the defects of a PTEN mutant. We have performed an initial test of this hypothesis in the model system Dictyostelium discoideum, which contains an ortholog of human PTEN, ptenA. Deletion of ptenA results in defects in motility, chemotaxis, aggregation and multicellular morphogenesis. D. discoideum also contains lpten, a newly discovered homolog of ptenA. Overexpressing lpten completely rescues all developmental and behavioral defects of the D. discoideum mutant ptenA−. This hypothesis must now be tested in human cells.
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Affiliation(s)
- Daniel F. Lusche
- Monoclonal Antibody Research Institute and Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Deborah Wessels
- Monoclonal Antibody Research Institute and Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Nicole A. Richardson
- Monoclonal Antibody Research Institute and Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Kanoe B. Russell
- Monoclonal Antibody Research Institute and Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Brett M. Hanson
- Monoclonal Antibody Research Institute and Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Benjamin A. Soll
- Monoclonal Antibody Research Institute and Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Benjamin H. Lin
- Monoclonal Antibody Research Institute and Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
| | - David R. Soll
- Monoclonal Antibody Research Institute and Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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62
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Simon M, Plattner H. Unicellular Eukaryotes as Models in Cell and Molecular Biology. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 309:141-98. [DOI: 10.1016/b978-0-12-800255-1.00003-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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63
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Annesley SJ, Chen S, Francione LM, Sanislav O, Chavan AJ, Farah C, De Piazza SW, Storey CL, Ilievska J, Fernando SG, Smith PK, Lay ST, Fisher PR. Dictyostelium, a microbial model for brain disease. Biochim Biophys Acta Gen Subj 2013; 1840:1413-32. [PMID: 24161926 DOI: 10.1016/j.bbagen.2013.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/05/2013] [Accepted: 10/10/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND Most neurodegenerative diseases are associated with mitochondrial dysfunction. In humans, mutations in mitochondrial genes result in a range of phenotypic outcomes which do not correlate well with the underlying genetic cause. Other neurodegenerative diseases are caused by mutations that affect the function and trafficking of lysosomes, endosomes and autophagosomes. Many of the complexities of these human diseases can be avoided by studying them in the simple eukaryotic model Dictyostelium discoideum. SCOPE OF REVIEW This review describes research using Dictyostelium to study cytopathological pathways underlying a variety of neurodegenerative diseases including mitochondrial, lysosomal and vesicle trafficking disorders. MAJOR CONCLUSIONS Generalised mitochondrial respiratory deficiencies in Dictyostelium produce a consistent pattern of defective phenotypes that are caused by chronic activation of a cellular energy sensor AMPK (AMP-activated protein kinase) and not ATP deficiency per se. Surprisingly, when individual subunits of Complex I are knocked out, both AMPK-dependent and AMPK-independent, subunit-specific phenotypes are observed. Many nonmitochondrial proteins associated with neurological disorders have homologues in Dictyostelium and are associated with the function and trafficking of lysosomes and endosomes. Conversely, some genes associated with neurodegenerative disorders do not have homologues in Dictyostelium and this provides a unique avenue for studying these mutated proteins in the absence of endogeneous protein. GENERAL SIGNIFICANCE Using the Dictyostelium model we have gained insights into the sublethal cytopathological pathways whose dysregulation contributes to phenotypic outcomes in neurodegenerative disease. This work is beginning to distinguish correlation, cause and effect in the complex network of cross talk between the various organelles involved. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.
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Affiliation(s)
- S J Annesley
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - S Chen
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - L M Francione
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - O Sanislav
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - A J Chavan
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - C Farah
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - S W De Piazza
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - C L Storey
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - J Ilievska
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - S G Fernando
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - P K Smith
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - S T Lay
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086
| | - P R Fisher
- Department of Microbiology, La Trobe University, Plenty Rd., Bundoora, VIC, Australia, 3086.
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Identification of Pentatricopeptide Repeat Proteins in the Model Organism Dictyostelium discoideum. Int J Genomics 2013; 2013:586498. [PMID: 23998118 PMCID: PMC3753752 DOI: 10.1155/2013/586498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are RNA binding proteins with functions in organelle RNA metabolism. They are found in all eukaryotes but have been most extensively studied in plants. We report on the identification of 12 PPR-encoding genes in the genome of the protist Dictyostelium discoideum, with potential homologs in other members of the same lineage and some predicted novel functions for the encoded gene products in protists. For one of the gene products, we show that it localizes to the mitochondria, and we also demonstrate that antisense inhibition of its expression leads to slower growth, a phenotype associated with mitochondrial dysfunction.
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65
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Manna S, Le P, Barth C. A unique mitochondrial transcription factor B protein in Dictyostelium discoideum. PLoS One 2013; 8:e70614. [PMID: 23923009 PMCID: PMC3724811 DOI: 10.1371/journal.pone.0070614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022] Open
Abstract
Unlike their bacteriophage homologs, mitochondrial RNA polymerases require the assistance of transcription factors in order to transcribe mitochondrial DNA efficiently. The transcription factor A family has been shown to be important for transcription of the human mitochondrial DNA, with some of its regulatory activity located in its extended C-terminal tail. The mitochondrial transcription factor B family often has functions not only in transcription, but also in mitochondrial rRNA modification, a hallmark of its α-proteobacterial origin. We have identified and characterised a mitochondrial transcription factor B homolog in the soil dwelling cellular slime mould Dictyostelium discoideum, an organism widely established as a model for studying eukaryotic cell biology. Using in bacterio functional assays, we demonstrate that the mitochondrial transcription factor B homolog not only functions as a mitochondrial transcription factor, but that it also has a role in rRNA methylation. Additionally, we show that the transcriptional activation properties of the D. discoideum protein are located in its extended C-terminal tail, a feature not seen before in the mitochondrial transcription factor B family, but reminiscent of the human mitochondrial transcription factor A. This report contributes to our current understanding of the complexities of mitochondrial transcription, and its evolution in eukaryotes.
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Affiliation(s)
- Sam Manna
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Phuong Le
- Tokyo Metropolitan University, Department of Biological Science, Tokyo, Japan
| | - Christian Barth
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia
- * E-mail:
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66
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Thewes S, Schubert SK, Park K, Mutzel R. Stress and development inDictyostelium discoideum: the involvement of the catalytic calcineurin A subunit. J Basic Microbiol 2013; 54:607-13. [DOI: 10.1002/jobm.201200574] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/19/2013] [Indexed: 01/26/2023]
Affiliation(s)
- Sascha Thewes
- Department of Biology, Chemistry, Pharmacy; Institute for Biology - Microbiology, Freie Universität Berlin; Berlin Germany
| | - Sebastian K. Schubert
- Department of Biology, Chemistry, Pharmacy; Institute for Biology - Microbiology, Freie Universität Berlin; Berlin Germany
| | - Kyuhyeon Park
- Department of Biology, Chemistry, Pharmacy; Institute for Biology - Microbiology, Freie Universität Berlin; Berlin Germany
| | - Rupert Mutzel
- Department of Biology, Chemistry, Pharmacy; Institute for Biology - Microbiology, Freie Universität Berlin; Berlin Germany
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67
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Lebeaux D, Chauhan A, Rendueles O, Beloin C. From in vitro to in vivo Models of Bacterial Biofilm-Related Infections. Pathogens 2013; 2:288-356. [PMID: 25437038 PMCID: PMC4235718 DOI: 10.3390/pathogens2020288] [Citation(s) in RCA: 308] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/01/2013] [Accepted: 05/08/2013] [Indexed: 12/13/2022] Open
Abstract
The influence of microorganisms growing as sessile communities in a large number of human infections has been extensively studied and recognized for 30–40 years, therefore warranting intense scientific and medical research. Nonetheless, mimicking the biofilm-life style of bacteria and biofilm-related infections has been an arduous task. Models used to study biofilms range from simple in vitro to complex in vivo models of tissues or device-related infections. These different models have progressively contributed to the current knowledge of biofilm physiology within the host context. While far from a complete understanding of the multiple elements controlling the dynamic interactions between the host and biofilms, we are nowadays witnessing the emergence of promising preventive or curative strategies to fight biofilm-related infections. This review undertakes a comprehensive analysis of the literature from a historic perspective commenting on the contribution of the different models and discussing future venues and new approaches that can be merged with more traditional techniques in order to model biofilm-infections and efficiently fight them.
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Affiliation(s)
- David Lebeaux
- Institut Pasteur, Unité de Génétique des Biofilms, 25 rue du Dr. Roux, 75724 Paris cedex 15, France.
| | - Ashwini Chauhan
- Institut Pasteur, Unité de Génétique des Biofilms, 25 rue du Dr. Roux, 75724 Paris cedex 15, France.
| | - Olaya Rendueles
- Institut Pasteur, Unité de Génétique des Biofilms, 25 rue du Dr. Roux, 75724 Paris cedex 15, France.
| | - Christophe Beloin
- Institut Pasteur, Unité de Génétique des Biofilms, 25 rue du Dr. Roux, 75724 Paris cedex 15, France.
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68
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Erken M, Lutz C, McDougald D. The rise of pathogens: predation as a factor driving the evolution of human pathogens in the environment. MICROBIAL ECOLOGY 2013; 65:860-8. [PMID: 23354181 PMCID: PMC3637895 DOI: 10.1007/s00248-013-0189-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 01/14/2013] [Indexed: 05/08/2023]
Abstract
Bacteria in the environment must survive predation from bacteriophage, heterotrophic protists, and predatory bacteria. This selective pressure has resulted in the evolution of a variety of defense mechanisms, which can also function as virulence factors. Here we discuss the potential dual function of some of the mechanisms, which protect against heterotrophic protists, and how predation pressure leads to the evolution of pathogenicity. This is in accordance with the coincidental evolution hypothesis, which suggests that virulence factors arose as a response to other selective pressures, for example, predation rather than for virulence per se. In this review we discuss some of those environmental factors that may be associated with the rise of pathogens in the marine environment. In particular, we will discuss the role of heterotrophic protists in the evolution of virulence factors in marine bacteria. Finally, we will discuss the implications for expansion of current pathogens and emergence of new pathogens.
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Affiliation(s)
- Martina Erken
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, New South Wales 2052 Australia
| | - Carla Lutz
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, New South Wales 2052 Australia
| | - Diane McDougald
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, New South Wales 2052 Australia
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, School of Biological Sciences, Nanyang Technological University, Nanyang Avenue, Singapore, 637551 Singapore
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69
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Carilla-Latorre S, Annesley SJ, Muñoz-Braceras S, Fisher PR, Escalante R. Ndufaf5 deficiency in the Dictyostelium model: new roles in autophagy and development. Mol Biol Cell 2013; 24:1519-28. [PMID: 23536703 PMCID: PMC3655813 DOI: 10.1091/mbc.e12-11-0796] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ndufaf5 is a conserved protein mutated in patients with mitochondrial complex I (CI) disease. A Dictyostelium model lacking functional Ndufaf5 provides new insights into the cytopathology of the disease, including a specific CI deficiency, AMPK-independent defects in growth and development, and a connection with autophagy. Ndufaf5 (also known as C20orf7) is a mitochondrial complex I (CI) assembly factor whose mutations lead to human mitochondrial disease. Little is known about the function of the protein and the cytopathological consequences of the mutations. Disruption of Dictyostelium Ndufaf5 leads to CI deficiency and defects in growth and development. The predicted sequence of Ndufaf5 contains a putative methyltransferase domain. Site-directed mutagenesis indicates that the methyltransferase motif is essential for its function. Pathological mutations were recreated in the Dictyostelium protein and expressed in the mutant background. These proteins were unable to complement the phenotypes, which further validates Dictyostelium as a model of the disease. Chronic activation of AMP-activated protein kinase (AMPK) has been proposed to play a role in Dictyostelium and human cytopathology in mitochondrial diseases. However, inhibition of the expression of AMPK gene in the Ndufaf5-null mutant does not rescue the phenotypes associated with the lack of Ndufaf5, suggesting that novel AMPK-independent pathways are responsible for Ndufaf5 cytopathology. Of interest, the Ndufaf5-deficient strain shows an increase in autophagy. This phenomenon was also observed in a Dictyostelium mutant lacking MidA (C2orf56/PRO1853/Ndufaf7), another CI assembly factor, suggesting that autophagy activation might be a common feature in mitochondrial CI dysfunction.
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Affiliation(s)
- Sergio Carilla-Latorre
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28029 Madrid, Spain
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70
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Actin cytoskeleton of chemotactic amoebae operates close to the onset of oscillations. Proc Natl Acad Sci U S A 2013; 110:3853-8. [PMID: 23431176 DOI: 10.1073/pnas.1216629110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rapid reorganization of the actin cytoskeleton in response to external stimuli is an essential property of many motile eukaryotic cells. Here, we report evidence that the actin machinery of chemotactic Dictyostelium cells operates close to an oscillatory instability. When averaging the actin response of many cells to a short pulse of the chemoattractant cAMP, we observed a transient accumulation of cortical actin reminiscent of a damped oscillation. At the single-cell level, however, the response dynamics ranged from short, strongly damped responses to slowly decaying, weakly damped oscillations. Furthermore, in a small subpopulation, we observed self-sustained oscillations in the cortical F-actin concentration. To substantiate that an oscillatory mechanism governs the actin dynamics in these cells, we systematically exposed a large number of cells to periodic pulse trains of different frequencies. Our results indicate a resonance peak at a stimulation period of around 20 s. We propose a delayed feedback model that explains our experimental findings based on a time-delay in the regulatory network of the actin system. To test the model, we performed stimulation experiments with cells that express GFP-tagged fusion proteins of Coronin and actin-interacting protein 1, as well as knockout mutants that lack Coronin and actin-interacting protein 1. These actin-binding proteins enhance the disassembly of actin filaments and thus allow us to estimate the delay time in the regulatory feedback loop. Based on this independent estimate, our model predicts an intrinsic period of 20 s, which agrees with the resonance observed in our periodic stimulation experiments.
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71
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Kim J, Ennis HL, Nguyen TH, Zhuang X, Luo J, Yao J, Kessin RH, Stojanovic M, Lin Q. Light-Directed Migration of D. discoideum Slugs in Microfabricated Confinements. SENSORS AND ACTUATORS. A, PHYSICAL 2012; 188:312-319. [PMID: 24723742 PMCID: PMC3979551 DOI: 10.1016/j.sna.2011.12.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
This paper investigates the light-driven migration of the multi-cellular microorganism Dictyostelium discoideum as a potential bio-actuation mechanism in microsystems. As a platform for slug migration we use microscale confinements, which consist of intersecting microchannels fabricated from solidified agar-water solution. The agar surface provides necessary moisture to the slugs during the experiment while remaining sufficiently stiff to allow effective slug migration. The movements of the slugs in the microchannels are driven and guided by phototaxis via controlling light transmitted through optical fibers. The microchannels impose geometrical confinements on the migrating slugs, improving the spatial precision of the migration. We demonstrate that slugs that form in a microchamber can be driven to migrate through the microchannels, as well as steered to a particular direction at microchannel intersections. Our experimental results indicate that slug movements can be more effectively controlled in microchannels, and potentially useful for bio-actuation applications.
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Affiliation(s)
- Jinho Kim
- Department of Mechanical Engineering, Columbia University, New York, NY 10027
| | - Herbert L. Ennis
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032
| | - Thai Huu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, NY 10027
| | - Xuye Zhuang
- Institute of Optics and Electronics, Chinese Academy of Sciences, Chengdu, 610209, China
| | - Ji Luo
- Institute of Optics and Electronics, Chinese Academy of Sciences, Chengdu, 610209, China
| | - Jun Yao
- Institute of Optics and Electronics, Chinese Academy of Sciences, Chengdu, 610209, China
| | - Richard H. Kessin
- Department of Anatomy and Cell Biology, Columbia University, New York, NY 10032
| | - Milan Stojanovic
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027
- Corresponding Author: Columbia University, Department of Mechanical Engineering, 500 W 120 St, Mudd Rm 220, New York, NY, 10027; phone: 1-212-854-1906;
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72
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Simple system--substantial share: the use of Dictyostelium in cell biology and molecular medicine. Eur J Cell Biol 2012. [PMID: 23200106 DOI: 10.1016/j.ejcb.2012.10.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Dictyostelium discoideum offers unique advantages for studying fundamental cellular processes, host-pathogen interactions as well as the molecular causes of human diseases. The organism can be easily grown in large amounts and is amenable to diverse biochemical, cell biological and genetic approaches. Throughout their life cycle Dictyostelium cells are motile, and thus are perfectly suited to study random and directed cell motility with the underlying changes in signal transduction and the actin cytoskeleton. Dictyostelium is also increasingly used for the investigation of human disease genes and the crosstalk between host and pathogen. As a professional phagocyte it can be infected with several human bacterial pathogens and used to study the infection process. The availability of a large number of knock-out mutants renders Dictyostelium particularly useful for the elucidation and investigation of host cell factors. A powerful armory of molecular genetic techniques that have been continuously expanded over the years and a well curated genome sequence, which is accessible via the online database dictyBase, considerably strengthened Dictyostelium's experimental attractiveness and its value as model organism.
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73
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Saxer G, Havlak P, Fox SA, Quance MA, Gupta S, Fofanov Y, Strassmann JE, Queller DC. Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum. PLoS One 2012; 7:e46759. [PMID: 23056439 PMCID: PMC3466296 DOI: 10.1371/journal.pone.0046759] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/03/2012] [Indexed: 12/18/2022] Open
Abstract
Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10(-9), with a Poisson confidence interval of 4.1×10(-9) - 9.5×10(-9), per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10(-11), with a Poisson confidence interval ranging from 7.4×10(-13) to 1.6×10(-10), is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. discoideum and low levels of genetic variation observed in wild D. discoideum populations. In addition, D. discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.
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Affiliation(s)
- Gerda Saxer
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America.
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74
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Reactive oxygen species in the signaling and adaptation of multicellular microbial communities. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:976753. [PMID: 22829965 PMCID: PMC3395218 DOI: 10.1155/2012/976753] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 05/24/2012] [Indexed: 02/07/2023]
Abstract
One of the universal traits of microorganisms is their ability to form multicellular structures, the cells of which differentiate and communicate via various signaling molecules. Reactive oxygen species (ROS), and hydrogen peroxide in particular, have recently become well-established signaling molecules in higher eukaryotes, but still little is known about the regulatory functions of ROS in microbial structures. Here we summarize current knowledge on the possible roles of ROS during the development of colonies and biofilms, representatives of microbial multicellularity. In Saccharomyces cerevisiae colonies, ROS are predicted to participate in regulatory events involved in the induction of ammonia signaling and later on in programmed cell death in the colony center. While the latter process seems to be induced by the total ROS, the former event is likely to be regulated by ROS-homeostasis, possibly H2O2-homeostasis between the cytosol and mitochondria. In Candida albicans biofilms, the predicted signaling role of ROS is linked with quorum sensing molecule farnesol that significantly affects biofilm formation. In bacterial biofilms, ROS induce genetic variability, promote cell death in specific biofilm regions, and possibly regulate biofilm development. Thus, the number of examples suggesting ROS as signaling molecules and effectors in the development of microbial multicellularity is rapidly increasing.
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75
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Abstract
This review focuses on basic principles of motility in different cell types, formation of the specific cell structures that enable directed migration, and how external signals are transduced into cells and coupled to the motile machinery. Feedback mechanisms and their potential role in maintenance of internal chemotactic gradients and persistence of directed migration are highlighted.
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Affiliation(s)
- A V Vorotnikov
- Department of Biochemistry and Molecular Medicine, Lomonosov Moscow State University, Moscow, Russia.
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76
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Impact of the carbazole derivative wiskostatin on mechanical stability and dynamics of motile cells. J Muscle Res Cell Motil 2012; 33:95-106. [PMID: 22407517 DOI: 10.1007/s10974-012-9287-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/26/2012] [Indexed: 10/28/2022]
Abstract
Many essential functions in eukaryotic cells like phagocytosis, division, and motility rely on the dynamical properties of the actin cytoskeleton. A central player in the actin system is the Arp2/3 complex. Its activity is controlled by members of the WASP (Wiskott-Aldrich syndrome protein) family. In this work, we investigated the effect of the carbazole derivative wiskostatin, a recently identified N-WASP inhibitor, on actin-driven processes in motile cells of the social ameba Dictyostelium discoideum. Drug-treated cells exhibited an altered morphology and strongly reduced pseudopod formation. However, TIRF microscopy images revealed that the overall cortical network structure remained intact. We probed the mechanical stability of wiskostatin-treated cells using a microfluidic device. While the total amount of F-actin in the cells remained constant, their stiffness was strongly reduced. Furthermore, wiskostatin treatment enhanced the resistance to fluid shear stress, while spontaneous motility as well as chemotactic motion in gradients of cAMP were reduced. Our results suggest that wiskostatin affects the mechanical integrity of the actin cortex so that its rigidity is reduced and actin-driven force generation is impaired.
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77
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Kaufmann S, Weiss IM, Eckstein V, Tanaka M. Functional expression of Ca²⁺ dependent mammalian transmembrane gap junction protein Cx43 in slime mold Dictyostelium discoideum. Biochem Biophys Res Commun 2012; 419:165-9. [PMID: 22330805 DOI: 10.1016/j.bbrc.2012.01.126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/26/2012] [Indexed: 11/16/2022]
Abstract
In this paper, we expressed murine gap junction protein Cx43 in Dictyostelium discoideum by introducing the specific vector pDXA. In the first step, the successful expression of Cx43 and Cx43-eGFP was verified by (a) Western blot (anti-Cx43, anti-GFP), (b) fluorescence microscopy (eGFP-Cx43 co-expression, Cx43 immunostaining), and (c) flow cytometry analysis (eGFP-Cx43 co-expression). Although the fluorescence signals from cells expressing Cx43-eGFP detected by fluorescence microscopy seem relatively low, analysis by flow cytometry demonstrated that more than 60% of cells expressed Cx43-eGFP. In order to evaluate the function of expressed Cx43 in D. discoideum, we examined the hemi-channel function of Cx43. In this series of experiments, the passive uptake of carboxyfluorescein was monitored using flow cytometric analysis. A significant number of the transfected cells showed a prominent dye uptake in the absence of Ca(2+). The dye uptake by transfected cells in the presence of Ca(2+) was even lower than the non-specific dye uptake by non-transformed Ax3 orf+ cells, confirming that Cx43 expressed in D. discoideum retains its Ca(2+)-dependent, specific gating function. The expression of gap junction proteins expressed in slime molds opens a possibility to the biological significance of intercellular communications in development and maintenance of multicellular organisms.
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Affiliation(s)
- Stefan Kaufmann
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, University of Heidelberg, D69120 Heidelberg, Germany.
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78
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Dallaire-Dufresne S, Paquet VE, Charette SJ. [Dictyostelium discoideum: a model for the study of bacterial virulence]. Can J Microbiol 2012; 57:699-707. [PMID: 21877947 DOI: 10.1139/w11-072] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The amoeba Dictyostelium discoideum, a bacterial predator, has emerged as a valuable tool for studying bacterial virulence. All its features make this unicellular eukaryote a versatile model organism. It can be used to study virulence factors of pathogenic bacteria as well as host elements involved in resistance to pathogens. The virulence of more than 20 bacterial species pathogenic for humans or animals has been studied using D. discoideum so far. These bacteria are either extracellular or intracellular pathogens. This review presents an overview of the question, with special emphasis on the reasons why D. discoideum is a suitable host model to study bacterial virulence, as well as on the type of information on host–pathogen relationship this amoeba can provide.
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Affiliation(s)
- Stéphanie Dallaire-Dufresne
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Québec, QC G1V 0A6, Canada
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79
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Montagnes D, Roberts E, Lukeš J, Lowe C. The rise of model protozoa. Trends Microbiol 2012; 20:184-91. [PMID: 22342867 DOI: 10.1016/j.tim.2012.01.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 01/05/2012] [Accepted: 01/17/2012] [Indexed: 12/23/2022]
Abstract
It is timely to evaluate the role of protozoa as model organisms given their diversity, abundance and versatility as well as the economic and ethical pressures placed on animal-based experimentation. We first define the term model organism and then examine through examples why protozoa make good models. Our examples reflect major issues including evolution, ecology, population and community biology, disease, the role of organelles, ageing, space travel, toxicity and teaching. We conclude by recognising that although protozoa may in some cases not completely mimic tissue- or whole-animal-level processes, they are extremely flexible and their use should be embraced. Finally, we offer advice on obtaining emergent model protozoa.
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Affiliation(s)
- David Montagnes
- Institute of Integrative Biology, University of Liverpool, BioScience Building, Crown Street, Liverpool L69 7ZB, UK.
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80
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von Bülow J, Müller-Lucks A, Kai L, Bernhard F, Beitz E. Functional characterization of a novel aquaporin from Dictyostelium discoideum amoebae implies a unique gating mechanism. J Biol Chem 2012; 287:7487-94. [PMID: 22262860 DOI: 10.1074/jbc.m111.329102] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The social amoeba Dictyostelium discoideum is a widely used model organism for studying basic functions of protozoan and metazoan cells, such as osmoregulation and cell motility. There is evidence from other species that cellular water channels, aquaporins (AQP), are central to both processes. Yet, data on D. discoideum AQPs is almost absent. Despite cloning of two putative D. discoideum AQPs, WacA, and AqpA, water permeability has not been shown. Further, WacA and AqpA are expressed at the late multicellular stage and in spores but not in amoebae. We cloned a novel AQP, AqpB, from amoeboidal D. discoideum cells. Wild-type AqpB was impermeable to water, glycerol, and urea when expressed in Xenopus laevis oocytes. Neither stepwise truncation of the N terminus nor selected point mutations activated the water channel. However, mutational truncation by 12 amino acids of an extraordinary long intracellular loop induced water permeability of AqpB, hinting at a novel gating mechanism. This AqpB mutant was inhibited by mercuric chloride, confirming the presence of a cysteine residue in the selectivity filter as predicted by our structure model. We detected AqpB by Western blot analysis in a glycosylated and a non-glycosylated form throughout all developmental stages. When expressed in D. discoideum amoebae, AqpB-GFP fusion constructs localized to vacuolar structures, to the plasma membrane, and to lamellipodia-like membrane protrusions. We conclude that the localization pattern in conjunction with channel gating may be indicative of AqpB functions in osmoregulation as well as cell motility of D. discoideum.
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Affiliation(s)
- Julia von Bülow
- Department of Medicinal and Pharmaceutical Chemistry, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
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81
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Schönitzer V, Eichner N, Clausen-Schaumann H, Weiss IM. Transmembrane myosin chitin synthase involved in mollusc shell formation produced in Dictyostelium is active. Biochem Biophys Res Commun 2011; 415:586-90. [DOI: 10.1016/j.bbrc.2011.10.109] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 10/25/2011] [Indexed: 11/25/2022]
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82
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Annesley SJ, Bago R, Bosnar MH, Filic V, Marinović M, Weber I, Mehta A, Fisher PR. Dictyostelium discoideum nucleoside diphosphate kinase C plays a negative regulatory role in phagocytosis, macropinocytosis and exocytosis. PLoS One 2011; 6:e26024. [PMID: 21991393 PMCID: PMC3186806 DOI: 10.1371/journal.pone.0026024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 09/15/2011] [Indexed: 12/30/2022] Open
Abstract
Nucleoside diphosphate kinases (NDPKs) are ubiquitous phosphotransfer enzymes responsible for producing most of the nucleoside triphosphates except for ATP. This role is important for the synthesis of nucleic acids and proteins and the metabolism of sugars and lipids. Apart from this housekeeping role NDPKs have been shown to have many regulatory functions in diverse cellular processes including proliferation and endocytosis. Although the protein has been shown to have a positive regulatory role in clathrin- and dynamin-mediated micropinocytosis, its roles in macropinocytosis and phagocytosis have not been studied. The additional non-housekeeping roles of NDPK are often independent of enzyme activity but dependent on the expression level of the protein. In this study we altered the expression level of NDPK in the model eukaryotic organism Dictyostelium discoideum through antisense inhibition and overexpression. We demonstrate that NDPK levels affect growth, endocytosis and exocytosis. In particular we find that Dictyostelium NDPK negatively regulates endocytosis in contrast to the positive regulatory role identified in higher eukaryotes. This can be explained by the differences in types of endocytosis that have been studied in the different systems - phagocytosis and macropinocytosis in Dictyostelium compared with micropinocytosis in mammalian cells. This is the first report of a role for NDPK in regulating macropinocytosis and phagocytosis, the former being the major fluid phase uptake mechanism for macrophages, dendritic cells and other (non dendritic) cells exposed to growth factors.
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Affiliation(s)
| | - Ruzica Bago
- Department of Microbology, La Trobe University, Victoria, Australia
- Division of Molecular Medicine, Rudjer Bošković Institute, Zagreb, Croatia
| | - Maja Herak Bosnar
- Division of Molecular Medicine, Rudjer Bošković Institute, Zagreb, Croatia
| | - Vedrana Filic
- Division of Molecular Biology, Rudjer Bošković Institute, Zagreb, Croatia
| | - Maja Marinović
- Division of Molecular Biology, Rudjer Bošković Institute, Zagreb, Croatia
| | - Igor Weber
- Division of Molecular Biology, Rudjer Bošković Institute, Zagreb, Croatia
| | - Anil Mehta
- Division of Medical Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Paul R. Fisher
- Department of Microbology, La Trobe University, Victoria, Australia
- * E-mail:
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83
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Abstract
Chemotaxis of tumour cells and stromal cells in the surrounding microenvironment is an essential component of tumour dissemination during progression and metastasis. This Review summarizes how chemotaxis directs the different behaviours of tumour cells and stromal cells in vivo, how molecular pathways regulate chemotaxis in tumour cells and how chemotaxis choreographs cell behaviour to shape the tumour microenvironment and to determine metastatic spread. The central importance of chemotaxis in cancer progression is highlighted by discussion of the use of chemotaxis as a prognostic marker, a treatment end point and a target of therapeutic intervention.
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Affiliation(s)
- Evanthia T Roussos
- Department of Anatomy and Structural Biology, Program in Tumor Microenvironment and Metastasis, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
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84
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Abstract
The Gram-positive bacterium Streptococcus suis is a major swine pathogen worldwide that causes meningitis, septicemia, and endocarditis. In this study, we demonstrate that the amoeba Dictyostelium discoideum can be a relevant alternative system to study the virulence of S. suis.
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85
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Moncho-Amor V, Galardi-Castilla M, Perona R, Sastre L. The dual-specificity protein phosphatase MkpB, homologous to mammalian MKP phosphatases, is required for D. discoideum post-aggregative development and cisplatin response. Differentiation 2011; 81:199-207. [PMID: 21300429 DOI: 10.1016/j.diff.2011.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 01/07/2011] [Accepted: 01/09/2011] [Indexed: 10/18/2022]
Abstract
Dual-specificity protein phosphatases participate in signal transduction pathways inactivating mitogen-activated protein kinases (MAP kinases). These signaling pathways are of critical importance in the regulation of numerous biological processes, including cell proliferation, differentiation and development. The social ameba Dictyostelium discoideum harbors 14 genes coding for proteins containing regions very similar to the dual-specificity protein phosphatase domain. One of these genes, mkpB, additionally codes for a region similar to the Rhodanase domain, characteristic of animal MAP kinase-phosphatases, in its N-terminal region. Cells that over-express this gene show increased protein phosphatase activity. mkpB is expressed in D. discoideum ameba at growth but it is greatly induced at 12h of multicellular development. Although it is expressed in all the cells of developmental structures, mkpB mRNA is enriched in cells with a distribution typical of anterior-like cells. Cells that express a catalytically inactive mutant of MkpB grow and aggregate like wild-type cells but show a greatly impaired post-aggregative development. In addition, the expression of cell-type specific genes is very delayed, indicating that this protein plays an important role in cell differentiation and development. Cells expressing the MkpB catalytically inactive mutant show increased sensitivity to cisplatin, while cells over-expressing wild type MkpB, or MkpA, proteins or mutated in the MAP kinase erkB gene are more resistant to this chemotherapeutic drug, as also shown in human tumor cells.
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Affiliation(s)
- Verónica Moncho-Amor
- Instituto de Investigaciones Biomédicas, CSIC/UAM, C/ Arturo Duperie, 4, 28029 Madrid, Spain
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86
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Wang Y, Steimle PA, Ren Y, Ross CA, Robinson DN, Egelhoff TT, Sesaki H, Iijima M. Dictyostelium huntingtin controls chemotaxis and cytokinesis through the regulation of myosin II phosphorylation. Mol Biol Cell 2011; 22:2270-81. [PMID: 21562226 PMCID: PMC3128529 DOI: 10.1091/mbc.e10-11-0926] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
This work shows that huntingtin protein (Htt) regulates the phosphorylation status of myosin II during chemotaxis and cytokinesis through protein phosphatase 2A (PP2A). Our findings provide novel insights into the physiological function of Htt and the pathogenesis of Huntington's disease. Abnormalities in the huntingtin protein (Htt) are associated with Huntington's disease. Despite its importance, the function of Htt is largely unknown. We show that Htt is required for normal chemotaxis and cytokinesis in Dictyostelium discoideum. Cells lacking Htt showed slower migration toward the chemoattractant cAMP and contained lower levels of cortical myosin II, which is likely due to defects in dephosphorylation of myosin II mediated by protein phosphatase 2A (PP2A). htt− cells also failed to maintain myosin II in the cortex of the cleavage furrow, generating unseparated daughter cells connected through a thin cytoplasmic bridge. Furthermore, similar to Dictyostelium htt− cells, siRNA-mediated knockdown of human HTT also decreased the PP2A activity in HeLa cells. Our data indicate that Htt regulates the phosphorylation status of myosin II during chemotaxis and cytokinesis through PP2A.
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Affiliation(s)
- Yu Wang
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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87
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Hulme SE, Whitesides GM. Die Chemie und der Wurm: Caenorhabditis elegans als Plattform für das Zusammenführen von chemischer und biologischer Forschung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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88
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Hulme SE, Whitesides GM. Chemistry and the Worm: Caenorhabditis elegans as a Platform for Integrating Chemical and Biological Research. Angew Chem Int Ed Engl 2011; 50:4774-807. [DOI: 10.1002/anie.201005461] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Indexed: 12/15/2022]
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89
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Perina D, Bosnar MH, Bago R, Mikoč A, Harcet M, Deželjin M, Cetković H. Sponge non-metastatic Group I Nme gene/protein - structure and function is conserved from sponges to humans. BMC Evol Biol 2011; 11:87. [PMID: 21457554 PMCID: PMC3078890 DOI: 10.1186/1471-2148-11-87] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 04/01/2011] [Indexed: 12/31/2022] Open
Abstract
Background Nucleoside diphosphate kinases NDPK are evolutionarily conserved enzymes present in Bacteria, Archaea and Eukarya, with human Nme1 the most studied representative of the family and the first identified metastasis suppressor. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestor's genomic features. Recent studies show that sponges have a wide repertoire of genes many of which are involved in diseases in more complex metazoans. The original function of those genes and the way it has evolved in the animal lineage is largely unknown. Here we report new results on the metastasis suppressor gene/protein homolog from the marine sponge Suberites domuncula, NmeGp1Sd. The purpose of this study was to investigate the properties of the sponge Group I Nme gene and protein, and compare it to its human homolog in order to elucidate the evolution of the structure and function of Nme. Results We found that sponge genes coding for Group I Nme protein are intron-rich. Furthermore, we discovered that the sponge NmeGp1Sd protein has a similar level of kinase activity as its human homolog Nme1, does not cleave negatively supercoiled DNA and shows nonspecific DNA-binding activity. The sponge NmeGp1Sd forms a hexamer, like human Nme1, and all other eukaryotic Nme proteins. NmeGp1Sd interacts with human Nme1 in human cells and exhibits the same subcellular localization. Stable clones expressing sponge NmeGp1Sd inhibited the migratory potential of CAL 27 cells, as already reported for human Nme1, which suggests that Nme's function in migratory processes was engaged long before the composition of true tissues. Conclusions This study suggests that the ancestor of all animals possessed a NmeGp1 protein with properties and functions similar to evolutionarily recent versions of the protein, even before the appearance of true tissues and the origin of tumors and metastasis.
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Affiliation(s)
- Drago Perina
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
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90
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A genetic interaction between NDPK and AMPK in Dictyostelium discoideum that affects motility, growth and development. Naunyn Schmiedebergs Arch Pharmacol 2011; 384:341-9. [PMID: 21374069 PMCID: PMC3390704 DOI: 10.1007/s00210-011-0615-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 02/16/2011] [Indexed: 11/25/2022]
Abstract
Many of the expanding roles of nucleoside diphosphate kinase have been attributed to its ability to interact with other proteins. One proposal is an interaction with the cellular energy sensor AMP-activated protein kinase, and here, we apply the simple eukaryotic organism, Dictyostelium discoideum as a test model. Stable cotransformants were created in which NDPK expression was knocked down by antisense inhibition, and AMPK activity was chronically elevated either by constitutive overexpression of its active, catalytic domain (AMPKαT) or as a result of mitochondrial dysfunction (created by antisense inhibition of expression of a mitochondrial chaperone protein, chaperonin 60). To investigate a biochemical interaction, transformants were created which contained constructs expressing FLAG-NDPK and hexahistidine-tagged full-length AMPK or AMPKαT. The protein extract from these transformants was used in coimmunoprecipitations. Knock down of NDPK expression suppressed the phenotypic defects that are caused by AMPK hyperactivity resulting either from overexpression of AMPKαT or from mitochondrial dysfunction. These included rescue of defects in slug phototaxis, fruiting body morphology and growth in a liquid medium. Coimmunoprecipitation experiments failed to demonstrate a biochemical interaction between the two proteins. The results demonstrate a genetic interaction between NDPK and AMPK in Dictyostelium in that NDPK is required for the phenotypic effects of activated AMPK. Coimmunoprecipitations suggest that this interaction is not mediated by a direct interaction between the two proteins.
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91
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Reddy AK, Balne PK, Garg P, Sangwan VS, Das M, Krishna PV, Bagga B, Vemuganti GK. Dictyostelium polycephalum infection of human cornea. Emerg Infect Dis 2011; 16:1644-5. [PMID: 20875305 PMCID: PMC3294405 DOI: 10.3201/eid1610.100717] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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92
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Nhe1 is essential for potassium but not calcium facilitation of cell motility and the monovalent cation requirement for chemotactic orientation in Dictyostelium discoideum. EUKARYOTIC CELL 2011; 10:320-31. [PMID: 21239624 DOI: 10.1128/ec.00255-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In Dictyostelium discoideum, extracellular K+ or Ca2+ at a concentration of 40 or 20 mM, respectively, facilitates motility in the absence or presence of a spatial gradient of chemoattractant. Facilitation results in maximum velocity, cellular elongation, persistent translocation, suppression of lateral pseudopod formation, and myosin II localization in the posterior cortex. A lower threshold concentration of 15 mM K+ or Na or 5 mM Ca2+ is required for chemotactic orientation. Although the common buffer solutions used by D. discoideum researchers to study chemotaxis contain sufficient concentrations of cations for chemotactic orientation, the majority contain insufficient levels to facilitate motility. Here it has been demonstrated that Nhe1, a plasma membrane protein, is required for K+ but not Ca2+ facilitation of cell motility and for the lower K+ but not Ca2+ requirement for chemotactic orientation.
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93
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Huber R, O'Day DH. EGF-like peptide-enhanced cell motility in Dictyostelium functions independently of the cAMP-mediated pathway and requires active Ca2+/calmodulin signaling. Cell Signal 2010; 23:731-8. [PMID: 21195758 DOI: 10.1016/j.cellsig.2010.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Revised: 12/14/2010] [Accepted: 12/22/2010] [Indexed: 02/06/2023]
Abstract
Current knowledge suggests that cell movement in the eukaryotic slime mold Dictyostelium discoideum is mediated by different signaling pathways involving a number of redundant components. Our previous research has identified a specific motility-enhancing function for epidermal growth factor-like (EGFL) repeats in Dictyostelium, specifically for the EGFL repeats of cyrA, a matricellular, calmodulin (CaM)-binding protein in Dictyostelium. Using mutants of cAMP signaling (carA(-), carC(-), gpaB(-), gpbA(-)), the endogenous calcium (Ca(2+)) release inhibitor TMB-8, the CaM antagonist W-7, and a radial motility bioassay, we show that DdEGFL1, a synthetic peptide whose sequence is obtained from the first EGFL repeat of cyrA, functions independently of the cAMP-mediated signaling pathways to enhance cell motility through a mechanism involving Ca(2+) signaling, CaM, and RasG. We show that DdEGFL1 increases the amounts of polymeric myosin II heavy chain and actin in the cytoskeleton by 24.1±10.7% and 25.9±2.1% respectively and demonstrate a link between Ca(2+)/CaM signaling and cytoskeletal dynamics. Finally, our findings suggest that carA and carC mediate a brake mechanism during chemotaxis since DdEGFL1 enhanced the movement of carA(-)/carC(-) cells by 844±136% compared to only 106±6% for parental DH1 cells. Based on our data, this signaling pathway also appears to involve the G-protein β subunit, RasC, RasGEFA, and protein kinase B. Together, our research provides insight into the functionality of EGFL repeats in Dictyostelium and the signaling pathways regulating cell movement in this model organism. It also identifies several mechanistic components of DdEGFL1-enhanced cell movement, which may ultimately provide a model system for understanding EGFL repeat function in higher organisms.
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Affiliation(s)
- Robert Huber
- Department of Cell & Systems Biology, 25 Harbord Street, University of Toronto, Ontario, Canada.
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94
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Francione LM, Annesley SJ, Carilla-Latorre S, Escalante R, Fisher PR. The Dictyostelium model for mitochondrial disease. Semin Cell Dev Biol 2010; 22:120-30. [PMID: 21129494 DOI: 10.1016/j.semcdb.2010.11.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 11/19/2010] [Accepted: 11/24/2010] [Indexed: 12/31/2022]
Abstract
Mitochondrial diseases are a diverse family of genetic disorders caused by mutations affecting mitochondrial proteins encoded in either the nuclear or the mitochondrial genome. By impairing mitochondrial oxidative phosphorylation, they compromise cellular energy production and the downstream consequences in humans are a bewilderingly complex array of signs and symptoms that can affect any of the major organ systems in unpredictable combinations. This complexity and unpredictability has limited our understanding of the cytopathological consequences of mitochondrial dysfunction. By contrast, in Dictyostelium the mitochondrial disease phenotypes are consistent, measurable "readouts" of dysregulated intracellular signalling pathways. When the underlying genetic defects would produce coordinate, generalized deficiencies in multiple mitochondrial respiratory complexes, the disease phenotypes are mediated by chronic activation of an energy-sensing protein kinase, AMP-activated protein kinase (AMPK). This chronic AMPK hyperactivity maintains mitochondrial mass and cellular ATP concentrations at normal levels, but chronically impairs growth, cell cycle progression, multicellular development, photosensory and thermosensory signal transduction. It also causes the cells to support greater proliferation of the intracellular bacterial pathogen, Legionella pneumophila. Notably however, phagocytic and macropinocytic nutrient uptake are impervious both to AMPK signalling and to these types of mitochondrial dysfunction. Surprisingly, a Complex I-specific deficiency (midA knockout) not only causes the foregoing AMPK-mediated defects, but also produces a dramatic deficit in endocytic nutrient uptake accompanied by an additional secondary defect in growth. More restricted and specific phenotypic outcomes are produced by knocking out genes for nuclear-encoded mitochondrial proteins that are not required for respiration. The Dictyostelium model for mitochondrial disease has thus revealed consistent patterns of sublethal dysregulation of intracellular signalling pathways that are produced by different types of underlying mitochondrial dysfunction.
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95
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Maniak M. Dictyostelium as a model for human lysosomal and trafficking diseases. Semin Cell Dev Biol 2010; 22:114-9. [PMID: 21056680 DOI: 10.1016/j.semcdb.2010.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 10/27/2010] [Accepted: 11/01/2010] [Indexed: 11/17/2022]
Abstract
Dictyostelium cells are genetically haploid and therefore easily analyzed for mutant phenotypes. In the past, many tools and molecular markers have been developed for a quantitative and qualitative analysis of the endocytic pathway in these amoebae. This review outlines parallels and discrepancies between mutants in Dictyostelium, the corresponding mammalian cells and the symptoms of human patients affected by lysosomal and trafficking defects. Situations where knowledge from Dictyostelium may potentially help understand human disease and vice versa are also addressed.
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Affiliation(s)
- Markus Maniak
- Abteilung Zellbiologie, Universität Kassel, Kassel, Germany.
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96
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Pang TL, Chen FC, Weng YL, Liao HC, Yi YH, Ho CL, Lin CH, Chen MY. Costars, a Dictyostelium protein similar to the C-terminal domain of STARS, regulates the actin cytoskeleton and motility. J Cell Sci 2010; 123:3745-55. [PMID: 20940261 DOI: 10.1242/jcs.064709] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Through analysis of a chemotaxis mutant obtained from a genetic screen in Dictyostelium discoideum, we have identified a new gene involved in regulating cell migration and have named it costars (cosA). The 82 amino acid Costars protein sequence appears highly conserved among diverse species, and significantly resembles the C-terminal region of the striated muscle activator of Rho signaling (STARS), a mammalian protein that regulates the serum response factor transcriptional activity through actin binding and Rho GTPase activation. The cosA-null (cosA(-)) cells formed smooth plaques on bacterial lawns, produced abnormally small fruiting bodies when developed on the non-nutrient agar and displayed reduced migration towards the cAMP source in chemotactic assays. Analysis of cell motion in cAMP gradients revealed decreased speed but wild-type-like directional persistence of cosA(-) cells, suggesting a defect in the cellular machinery for motility rather than for chemotactic orientation. Consistent with this notion, cosA(-) cells exhibited changes in the actin cytoskeleton, showing aberrant distribution of F-actin in fluorescence cell staining and an increased amount of cytoskeleton-associated actin. Excessive pseudopod formation was also noted in cosA(-) cells facing chemoattractant gradients. Expressing cosA or its human counterpart mCostars eliminated abnormalities of cosA(-) cells. Together, our results highlight a role for Costars in modulating actin dynamics and cell motility.
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Affiliation(s)
- Te-Ling Pang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan
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97
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Galardi-Castilla M, Garciandía A, Suarez T, Sastre L. The Dictyostelium discoideum acaA gene is transcribed from alternative promoters during aggregation and multicellular development. PLoS One 2010; 5:e13286. [PMID: 20949015 PMCID: PMC2952602 DOI: 10.1371/journal.pone.0013286] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Extracellular cAMP is a key extracellular signaling molecule that regulates aggregation, cell differentiation and morphogenesis during multi-cellular development of the social amoeba Dictyostelium discoideum. This molecule is produced by three different adenylyl cyclases, encoded by the genes acaA, acrA and acgA, expressed at different stages of development and in different structures. METHODOLOGY/PRINCIPAL FINDINGS This article describes the characterization of the promoter region of the acaA gene, showing that it is transcribed from three different alternative promoters. The distal promoter, promoter 1, is active during the aggregation process while the more proximal promoters are active in tip-organiser and posterior regions of the structures. A DNA fragment containing the three promoters drove expression to these same regions and similar results were obtained by in situ hybridization. Analyses of mRNA expression by quantitative RT-PCR with specific primers for each of the three transcripts also demonstrated their different temporal patterns of expression. CONCLUSIONS/SIGNIFICANCE The existence of an aggregation-specific promoter can be associated with the use of cAMP as chemo-attractant molecule, which is specific for some Dictyostelium species. Expression at late developmental stages indicates that adenylyl cyclase A might play a more important role in post-aggregative development than previously considered.
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Affiliation(s)
- Maria Galardi-Castilla
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Cientificas/Universidad Autónoma de Madrid, Madrid, Spain
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98
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Catalano A, Luo W, Wang Y, O'Day DH. Synthesis and biological activity of peptides equivalent to the IP22 repeat motif found in proteins from Dictyostelium and Mimivirus. Peptides 2010; 31:1799-805. [PMID: 20624437 DOI: 10.1016/j.peptides.2010.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 07/03/2010] [Accepted: 07/05/2010] [Indexed: 11/24/2022]
Abstract
A novel IP22 repeat motif of unknown function was discovered previously that comprises almost the entire structure of cmbB, a calmodulin-binding protein from Dictyostelium discoideum. An analysis of over 2000 IP22 repeats across 130 different proteins from different species allowed us to define a prototypical IP22 repeat: I/LPxxhxxhxhxxxhxxxhxxxx (where L=leucine, I=isoleucine, h=any hydrophobic amino acid, x=any amino acid). Here we describe the synthesis of three peptide variants of the IP22 motif: IP22-1 (IPNSVTSLKFGDGFNQPLTPGT; 22aa); IP22-2 (LPSTLKTISLSNSTDKKIFKNS; 22aa); and, IP22-3 (IPKSLRSLFLGKGYNQPLEF; 20aa) plus a control peptide from the N-term of cmbB (HNMNPFSPQLDEKKNSHIVEY; 21aa). The structure and purity of synthesized peptides were verified by HPLC and mass spectrometry. The peptides all dose-dependently enhanced random cell motility and cAMP-mediated chemotaxis in Dictyostelium but IP22-3 was most effective peaking in activity around 50 μM. Fluorescein isothiocyanate (FITC)-conjugated IP22 peptides did not penetrate cells suggesting these peptides affect cell motility via cell surface interactions. Treatment of cells with FITC-IP22 peptides also led to enhanced cell motility equivalent to the non-conjugated peptides. Treatment of IP22-3-stimulated cells with 50 μM LY294002, 20 μM quinacrine or both suggests that IP22-3 requires both phosphoinositol 3-kinase and phospholipase A2 signaling to elicit its effects, a mechanism unique from EGFL motility enhancing peptides. The mechanism of action and potential uses of IP22 repeat peptides are discussed.
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Affiliation(s)
- Andrew Catalano
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord st., Toronto, Ontario, Canada, M5S 3G5
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99
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Charest PG, Shen Z, Lakoduk A, Sasaki AT, Briggs SP, Firtel RA. A Ras signaling complex controls the RasC-TORC2 pathway and directed cell migration. Dev Cell 2010; 18:737-49. [PMID: 20493808 DOI: 10.1016/j.devcel.2010.03.017] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 01/25/2010] [Accepted: 03/03/2010] [Indexed: 11/17/2022]
Abstract
Ras was found to regulate Dictyostelium chemotaxis, but the mechanisms that spatially and temporally control Ras activity during chemotaxis remain largely unknown. We report the discovery of a Ras signaling complex that includes the Ras guanine exchange factor (RasGEF) Aimless, RasGEFH, protein phosphatase 2A (PP2A), and a scaffold designated Sca1. The Sca1/RasGEF/PP2A complex is recruited to the plasma membrane in a chemoattractant- and F-actin-dependent manner and is enriched at the leading edge of chemotaxing cells where it regulates F-actin dynamics and signal relay by controlling the activation of RasC and the downstream target of rapamycin complex 2 (TORC2)-Akt/protein kinase B (PKB) pathway. In addition, PKB and PKB-related PKBR1 phosphorylate Sca1 and regulate the membrane localization of the Sca1/RasGEF/PP2A complex, and thereby RasC activity, in a negative feedback fashion. Thus, our study uncovered a molecular mechanism whereby RasC activity and the spatiotemporal activation of TORC2 are tightly controlled at the leading edge of chemotaxing cells.
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Affiliation(s)
- Pascale G Charest
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0380, USA
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Carilla-Latorre S, Gallardo ME, Annesley SJ, Calvo-Garrido J, Graña O, Accari SL, Smith PK, Valencia A, Garesse R, Fisher PR, Escalante R. MidA is a putative methyltransferase that is required for mitochondrial complex I function. J Cell Sci 2010; 123:1674-83. [DOI: 10.1242/jcs.066076] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dictyostelium and human MidA are homologous proteins that belong to a family of proteins of unknown function called DUF185. Using yeast two-hybrid screening and pull-down experiments, we showed that both proteins interact with the mitochondrial complex I subunit NDUFS2. Consistent with this, Dictyostelium cells lacking MidA showed a specific defect in complex I activity, and knockdown of human MidA in HEK293T cells resulted in reduced levels of assembled complex I. These results indicate a role for MidA in complex I assembly or stability. A structural bioinformatics analysis suggested the presence of a methyltransferase domain; this was further supported by site-directed mutagenesis of specific residues from the putative catalytic site. Interestingly, this complex I deficiency in a Dictyostelium midA− mutant causes a complex phenotypic outcome, which includes phototaxis and thermotaxis defects. We found that these aspects of the phenotype are mediated by a chronic activation of AMPK, revealing a possible role of AMPK signaling in complex I cytopathology.
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Affiliation(s)
- Sergio Carilla-Latorre
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
| | - M. Esther Gallardo
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
| | - Sarah J. Annesley
- Department of Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Javier Calvo-Garrido
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
| | - Osvaldo Graña
- O. G., Bioinformatics Unit, Structural Biology and Biocomputing Program, A. V., Structural Computational Biology Group, Structural Biology and Biocomputing Program, Centro Nacional de Investigaciones Oncológicas, C/ Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Sandra L. Accari
- Department of Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Paige K. Smith
- Department of Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alfonso Valencia
- O. G., Bioinformatics Unit, Structural Biology and Biocomputing Program, A. V., Structural Computational Biology Group, Structural Biology and Biocomputing Program, Centro Nacional de Investigaciones Oncológicas, C/ Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Rafael Garesse
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
| | - Paul R. Fisher
- Department of Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
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