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McCauley KB, Kukreja K, Tovar Walker AE, Jaffe AB, Klein AM. A map of signaling responses in the human airway epithelium. Cell Syst 2024; 15:307-321.e10. [PMID: 38508187 PMCID: PMC11031335 DOI: 10.1016/j.cels.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 11/14/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling-response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal cell and secretory cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell-cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Katherine B McCauley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA; Disease Area X, Biomedical Research, Novartis, Cambridge, MA 02139, USA
| | - Kalki Kukreja
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Aron B Jaffe
- Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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2
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Lopez K, Lai SWT, Lopez Gonzalez EDJ, Dávila RG, Shuck SC. Extracellular vesicles: A dive into their role in the tumor microenvironment and cancer progression. Front Cell Dev Biol 2023; 11:1154576. [PMID: 37025182 PMCID: PMC10071009 DOI: 10.3389/fcell.2023.1154576] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 04/08/2023] Open
Abstract
Extracellular vesicles (EVs) encompass a diverse set of membrane-derived particles released from cells and are found in numerous biological matrices and the extracellular space. Specific classes of EVs include apoptotic bodies, exosomes, and microvesicles, which vary in their size, origin, membrane protein expression, and interior cargo. EVs provide a mechanism for shuttling cargo between cells, which can influence cell physiology by transporting proteins, DNA, and RNA. EVs are an abundant component of the tumor microenvironment (TME) and are proposed to drive tumor growth and progression by communicating between fibroblasts, macrophages, and tumor cells in the TME. The cargo, source, and type of EV influences the pro- or anti-tumoral role of these molecules. Therefore, robust EV isolation and characterization techniques are required to ensure accurate elucidation of their association with disease. Here, we summarize different EV subclasses, methods for EV isolation and characterization, and a selection of current clinical trials studying EVs. We also review key studies exploring the role and impact of EVs in the TME, including how EVs mediate intercellular communication, drive cancer progression, and remodel the TME.
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3
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Moggio A, Schunkert H, Kessler T, Sager HB. Quo Vadis? Immunodynamics of Myeloid Cells after Myocardial Infarction. Int J Mol Sci 2022; 23. [PMID: 36555456 DOI: 10.3390/ijms232415814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Myocardial infarction (MI), a major contributor to worldwide morbidity and mortality, is caused by a lack of blood flow to the heart. Affected heart tissue becomes ischemic due to deficiency of blood perfusion and oxygen delivery. In case sufficient blood flow cannot be timely restored, cardiac injury with necrosis occurs. The ischemic/necrotic area induces a systemic inflammatory response and hundreds of thousands of leukocytes are recruited from the blood to the injured heart. The blood pool of leukocytes is rapidly depleted and urgent re-supply of these cells is needed. Myeloid cells are generated in the bone marrow (BM) and spleen, released into the blood, travel to sites of need, extravasate and accumulate inside tissues to accomplish various functions. In this review we focus on the "leukocyte supply chain" and will separately evaluate different myeloid cell compartments (BM, spleen, blood, heart) in steady state and after MI. Moreover, we highlight the local and systemic kinetics of extracellular factors, chemokines and danger signals involved in the regulation of production/generation, release, transportation, uptake, and activation of myeloid cells during the inflammatory phase of MI.
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4
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Guljamow A, Barchewitz T, Große R, Timm S, Hagemann M, Dittmann E. Diel Variations of Extracellular Microcystin Influence the Subcellular Dynamics of RubisCO in Microcystis aeruginosa PCC 7806. Microorganisms 2021; 9:1265. [PMID: 34200971 DOI: 10.3390/microorganisms9061265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/02/2022] Open
Abstract
The ubiquitous freshwater cyanobacterium Microcystis is remarkably successful, showing a high tolerance against fluctuations in environmental conditions. It frequently forms dense blooms which can accumulate significant amounts of the hepatotoxin microcystin, which plays an extracellular role as an infochemical but also acts intracellularly by interacting with proteins of the carbon metabolism, notably with the CO2 fixing enzyme RubisCO. Here we demonstrate a direct link between external microcystin and its intracellular targets. Monitoring liquid cultures of Microcystis in a diel experiment revealed fluctuations in the extracellular microcystin content that correlate with an increase in the binding of microcystin to intracellular proteins. Concomitantly, reversible relocation of RubisCO from the cytoplasm to the cell’s periphery was observed. These variations in RubisCO localization were especially pronounced with cultures grown at higher cell densities. We replicated these effects by adding microcystin externally to cultures grown under continuous light. Thus, we propose that microcystin may be part of a fast response to conditions of high light and low carbon that contribute to the metabolic flexibility and the success of Microcystis in the field.
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5
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Carozza JA, Brown JA, Böhnert V, Fernandez D, AlSaif Y, Mardjuki RE, Smith M, Li L. Structure-Aided Development of Small-Molecule Inhibitors of ENPP1, the Extracellular Phosphodiesterase of the Immunotransmitter cGAMP. Cell Chem Biol 2020; 27:1347-1358.e5. [PMID: 32726585 PMCID: PMC7680421 DOI: 10.1016/j.chembiol.2020.07.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/28/2020] [Accepted: 07/08/2020] [Indexed: 11/23/2022]
Abstract
Cancer cells initiate an innate immune response by synthesizing and exporting the small-molecule immunotransmitter cGAMP, which activates the anti-cancer Stimulator of Interferon Genes (STING) pathway in the host. An extracellular enzyme, ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1), hydrolyzes cGAMP and negatively regulates this anti-cancer immune response. Small-molecule ENPP1 inhibitors are much needed as tools to study the basic biology of extracellular cGAMP and as investigational cancer immunotherapy drugs. Here, we surveyed structure-activity relationships around a series of cell-impermeable and thus extracellular-targeting phosphonate inhibitors of ENPP1. In addition, we solved the crystal structure of an exemplary phosphonate inhibitor to elucidate the interactions that drive potency. This study yielded several best-in-class inhibitors with Ki < 2 nM and excellent physicochemical and pharmacokinetic properties. Finally, we demonstrate that an ENPP1 inhibitor delays tumor growth in a breast cancer mouse model. Together, we have developed ENPP1 inhibitors that are excellent tool compounds and potential therapeutics.
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MESH Headings
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Cell Survival/drug effects
- Cells, Cultured
- Dose-Response Relationship, Drug
- Drug Screening Assays, Antitumor
- Enzyme Inhibitors/chemical synthesis
- Enzyme Inhibitors/chemistry
- Enzyme Inhibitors/pharmacology
- Female
- Humans
- Mice
- Mice, Inbred C57BL
- Molecular Structure
- Neoplasms, Experimental/drug therapy
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Neurotransmitter Agents/chemistry
- Neurotransmitter Agents/isolation & purification
- Neurotransmitter Agents/metabolism
- Nucleotides, Cyclic/chemistry
- Nucleotides, Cyclic/isolation & purification
- Nucleotides, Cyclic/metabolism
- Phosphoric Diester Hydrolases/metabolism
- Pyrophosphatases/antagonists & inhibitors
- Pyrophosphatases/metabolism
- Small Molecule Libraries/chemical synthesis
- Small Molecule Libraries/chemistry
- Small Molecule Libraries/pharmacology
- Structure-Activity Relationship
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Affiliation(s)
- Jacqueline A Carozza
- Department of Chemistry, Stanford University, Stanford, CA 93405, USA; Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA
| | - Jenifer A Brown
- Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA; Biophysics Program, Stanford University, Stanford, CA 93405, USA
| | - Volker Böhnert
- Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA; Department of Biochemistry, Stanford University, Stanford, CA 93405, USA
| | - Daniel Fernandez
- Stanford ChEM-H Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA 93405, USA
| | - Yasmeen AlSaif
- Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA; Department of Biology, Stanford University, Stanford, CA 93405, USA
| | - Rachel E Mardjuki
- Department of Chemistry, Stanford University, Stanford, CA 93405, USA; Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA
| | - Mark Smith
- Stanford ChEM-H Medicinal Chemistry Knowledge Center, Stanford, CA 93405, USA
| | - Lingyin Li
- Stanford ChEM-H, Stanford University, Stanford, CA 93405, USA; Department of Biochemistry, Stanford University, Stanford, CA 93405, USA.
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Abstract
INTRODUCTION Studying immune signaling has been critical for our understanding of immunology, pathogenesis, cancer, and homeostasis. To enhance the breadth of the analysis, high throughput methods have been developed to survey multiple areas simultaneously, including transcriptomics, reporter assays, and ELISAs. While these techniques have been extremely informative, mass-spectrometry-based technologies have been gaining momentum and starting to be widely used in the studies of immune signaling and systems immunology. AREAS COVERED We present established proteomic methods that have been used to address immune signaling and discuss the new mass-spectrometry- based techniques of interest to the expanding field of systems immunology. Established and new proteomic methods and their applications discussed here include post-translational modification analysis, protein quantification, secretome analysis, and interactomics. In addition, we present developments in small molecule and metabolite analysis, mass spectrometry imaging, and single cell analysis. Finally, we discuss the role of multi-omic integration in aiding leading edge investigation. EXPERT OPINION In science, available techniques enhance the breadth and depth of the studies. By incorporating proteomic techniques and their innovative use, it will be possible to expand the current studies and to address novel questions at the forefront of scientific discovery.
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Affiliation(s)
- Joseph Gillen
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
| | - Caleb Bridgwater
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, MD, USA
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Park H, Yamamoto Y, Tanaka-Yamamoto K. Refinement of Cerebellar Network Organization by Extracellular Signaling During Development. Neuroscience 2021; 462:44-55. [PMID: 32502568 DOI: 10.1016/j.neuroscience.2020.05.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022]
Abstract
The cerebellum forms regular neural network structures consisting of a few major types of neurons, such as Purkinje cells, granule cells, and molecular layer interneurons, and receives two major inputs from climbing fibers and mossy fibers. Its regular structures consist of three well-defined layers, with each type of neuron designated to a specific location and forming specific synaptic connections. During the first few weeks of postnatal development in rodents, the cerebellum goes through dynamic changes via proliferation, migration, differentiation, synaptogenesis, and maturation, to create such a network structure. The development of this organized network structure presumably relies on the communication between developing elements in the network, including not only individual neurons, but also their dendrites, axons, and synapses. Therefore, it is reasonable that extracellular signaling via synaptic transmission, secreted molecules, and cell adhesion molecules, plays important roles in cerebellar network development. Although it is not yet clear as to how overall cerebellar development is orchestrated, there is indeed accumulating lines of evidence that extracellular signaling acts toward the development of individual elements in the cerebellar networks. In this article, we introduce what we have learned from many studies regarding the extracellular signaling required for cerebellar network development, including our recent study suggesting the importance of unbiased synaptic inputs from parallel fibers.
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8
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Poiana G, Gioia R, Sineri S, Cardarelli S, Lupo G, Cacci E. Transcriptional regulation of adult neural stem/progenitor cells: tales from the subventricular zone. Neural Regen Res 2020; 15:1773-1783. [PMID: 32246617 PMCID: PMC7513981 DOI: 10.4103/1673-5374.280301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In rodents, well characterized neurogenic niches of the adult brain, such as the subventricular zone of the lateral ventricles and the subgranular zone of the hippocampus, support the maintenance of neural/stem progenitor cells (NSPCs) and the production of new neurons throughout the lifespan. The adult neurogenic process is dependent on the intrinsic gene expression signatures of NSPCs that make them competent for self-renewal and neuronal differentiation. At the same time, it is receptive to regulation by various extracellular signals that allow the modulation of neuronal production and integration into brain circuitries by various physiological stimuli. A drawback of this plasticity is the sensitivity of adult neurogenesis to alterations of the niche environment that can occur due to aging, injury or disease. At the core of the molecular mechanisms regulating neurogenesis, several transcription factors have been identified that maintain NSPC identity and mediate NSPC response to extrinsic cues. Here, we focus on REST, Egr1 and Dbx2 and their roles in adult neurogenesis, especially in the subventricular zone. We review recent work from our and other laboratories implicating these transcription factors in the control of NSPC proliferation and differentiation and in the response of NSPCs to extrinsic influences from the niche. We also discuss how their altered regulation may affect the neurogenic process in the aged and in the diseased brain. Finally, we highlight key open questions that need to be addressed to foster our understanding of the transcriptional mechanisms controlling adult neurogenesis.
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Affiliation(s)
- Giancarlo Poiana
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Roberta Gioia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Serena Sineri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Silvia Cardarelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Giuseppe Lupo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Emanuele Cacci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
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9
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Alijagic A, Benada O, Kofroňová O, Cigna D, Pinsino A. Sea Urchin Extracellular Proteins Design a Complex Protein Corona on Titanium Dioxide Nanoparticle Surface Influencing Immune Cell Behavior. Front Immunol 2019; 10:2261. [PMID: 31616433 PMCID: PMC6763604 DOI: 10.3389/fimmu.2019.02261] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/06/2019] [Indexed: 01/07/2023] Open
Abstract
Extensive exploitation of titanium dioxide nanoparticles (TiO2NPs) augments rapid release into the marine environment. When in contact with the body fluids of marine invertebrates, TiO2NPs undergo a transformation and adhere various organic molecules that shape a complex protein corona prior to contacting cells and tissues. To elucidate the potential extracellular signals that may be involved in the particle recognition by immune cells of the sea urchin Paracentrotus lividus, we investigated the behavior of TiO2NPs in contact with extracellular proteins in vitro. Our findings indicate that TiO2NPs are able to interact with sea urchin proteins in both cell-free and cell-conditioned media. The two-dimensional proteome analysis of the protein corona bound to TiO2NP revealed that negatively charged proteins bound preferentially to the particles. The main constituents shaping the sea urchin cell-conditioned TiO2NP protein corona were proteins involved in cellular adhesion (Pl-toposome, Pl-galectin-8, Pl-nectin) and cytoskeletal organization (actin and tubulin). Immune cells (phagocytes) aggregated TiO2NPs on the outer cell surface and within well-organized vesicles without eliciting harmful effects on the biological activities of the cells. Cells showed an active metabolism, no oxidative stress or caspase activation. These results provide a new level of understanding of the extracellular proteins involved in the immune-TiO2NP recognition and interaction in vitro, confirming that primary immune cell cultures from P. lividus can be an optional model for swift and efficient immune-toxicological investigations.
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Affiliation(s)
- Andi Alijagic
- Istituto per la Ricerca e l'Innovazione Biomedica (IRIB), Consiglio Nazionale delle Ricerche, Palermo, Italy
| | - Oldřich Benada
- Institute of Microbiology of The Czech Academy of Sciences, Prague, Czechia
| | - Olga Kofroňová
- Institute of Microbiology of The Czech Academy of Sciences, Prague, Czechia
| | - Diego Cigna
- Istituto per la Ricerca e l'Innovazione Biomedica (IRIB), Consiglio Nazionale delle Ricerche, Palermo, Italy
| | - Annalisa Pinsino
- Istituto per la Ricerca e l'Innovazione Biomedica (IRIB), Consiglio Nazionale delle Ricerche, Palermo, Italy
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10
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Ho TD, Nauta KM, Müh U, Ellermeier CD. Activation of the Extracytoplasmic Function σ Factor σ P by β-Lactams in Bacillus thuringiensis Requires the Site-2 Protease RasP. mSphere 2019; 4:e00511-19. [PMID: 31391284 DOI: 10.1128/mSphere.00511-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The discovery of antibiotics to treat bacterial infections has had a dramatic and positive impact on human health. However, shortly after the introduction of a new antibiotic, bacteria often develop resistance. The bacterial cell envelope is essential for cell viability and is the target of many of the most commonly used antibiotics, including β-lactam antibiotics. Resistance to β-lactams is often dependent upon β-lactamases. In B. cereus, B. thuringiensis, and some B. anthracis strains, the expression of some β-lactamases is inducible. This inducible β-lactamase expression is controlled by activation of an alternative σ factor called σP. Here, we show that β-lactam antibiotics induce σP activation by degradation of the anti-σ factor RsiP. Bacteria can utilize alternative σ factors to regulate sets of genes in response to changes in the environment. The largest and most diverse group of alternative σ factors are the extracytoplasmic function (ECF) σ factors. σP is an ECF σ factor found in Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis. Previous work showed that σP is induced by ampicillin, a β-lactam antibiotic, and required for resistance to ampicillin. However, it was not known how activation of σP is controlled or what other antibiotics may activate σP. Here, we report that activation of σP is specific to a subset of β-lactams and that σP is required for resistance to these β-lactams. We demonstrate that activation of σP is controlled by the proteolytic destruction of the anti-σ factor RsiP and that degradation of RsiP requires multiple proteases. Upon exposure to β-lactams, the extracellular domain of RsiP is cleaved by an unknown protease, which we predict cleaves at site-1. Following cleavage by the unknown protease, the N terminus of RsiP is further degraded by the site-2 intramembrane protease RasP. Our data indicate that RasP cleavage of RsiP is not the rate-limiting step in σP activation. This proteolytic cascade leads to activation of σP, which induces resistance to β-lactams likely via increased expression of β-lactamases. IMPORTANCE The discovery of antibiotics to treat bacterial infections has had a dramatic and positive impact on human health. However, shortly after the introduction of a new antibiotic, bacteria often develop resistance. The bacterial cell envelope is essential for cell viability and is the target of many of the most commonly used antibiotics, including β-lactam antibiotics. Resistance to β-lactams is often dependent upon β-lactamases. In B. cereus, B. thuringiensis, and some B. anthracis strains, the expression of some β-lactamases is inducible. This inducible β-lactamase expression is controlled by activation of an alternative σ factor called σP. Here, we show that β-lactam antibiotics induce σP activation by degradation of the anti-σ factor RsiP.
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11
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Mike LA. mSphere of Influence: Systematically Decoding Microbial Chemical Communication. mSphere 2019; 4:e00319-19. [PMID: 31292231 DOI: 10.1128/mSphere.00319-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laura A. Mike works in the field of bacterial pathogenesis. In this mSphere of Influence article, she reflects on how “Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters” by P. Cimermancic et al. (Cell 158:412–421, 2014, https://doi.org/10.1016/j.cell.2014.06.034) and “A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics” by M. S. Donia et al. (Cell 158:1402–1414, 2014, https://doi.org/10.1016/j.cell.2014.08.032) made an impact on her by systematically identifying microbiome-associated biosynthetic gene clusters predicted to synthesize secondary metabolites, which may facilitate interspecies interactions. Laura A. Mike works in the field of bacterial pathogenesis. In this mSphere of Influence article, she reflects on how “Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters” by P. Cimermancic et al. (Cell 158:412–421, 2014, https://doi.org/10.1016/j.cell.2014.06.034) and “A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics” by M. S. Donia et al. (Cell 158:1402–1414, 2014, https://doi.org/10.1016/j.cell.2014.08.032) made an impact on her by systematically identifying microbiome-associated biosynthetic gene clusters predicted to synthesize secondary metabolites, which may facilitate interspecies interactions.
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12
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Igler C, Abedon ST. Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision. Front Microbiol 2019; 10:1171. [PMID: 31214137 PMCID: PMC6557168 DOI: 10.3389/fmicb.2019.01171] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/07/2019] [Indexed: 01/21/2023] Open
Affiliation(s)
- Claudia Igler
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH, United States
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13
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Singh A, Mia MM, Cibi DM, Arya AK, Bhadada SK, Singh MK. Deficiency in the secreted protein Semaphorin3d causes abnormal parathyroid development in mice. J Biol Chem 2019; 294:8336-8347. [PMID: 30979723 DOI: 10.1074/jbc.ra118.007063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/09/2019] [Indexed: 12/31/2022] Open
Abstract
Primary hyperparathyroidism (PHPT) is a common endocrinopathy characterized by hypercalcemia and elevated levels of parathyroid hormone. The primary cause of PHPT is a benign overgrowth of parathyroid tissue causing excessive secretion of parathyroid hormone. However, the molecular etiology of PHPT is incompletely defined. Here, we demonstrate that semaphorin3d (Sema3d), a secreted glycoprotein, is expressed in the developing parathyroid gland in mice. We also observed that genetic deletion of Sema3d leads to parathyroid hyperplasia, causing PHPT. In vivo and in vitro experiments using histology, immunohistochemistry, biochemical, RT-qPCR, and immunoblotting assays revealed that Sema3d inhibits parathyroid cell proliferation by decreasing the epidermal growth factor receptor (EGFR)/Erb-B2 receptor tyrosine kinase (ERBB) signaling pathway. We further demonstrate that EGFR signaling is elevated in Sema3d -/- parathyroid glands and that pharmacological inhibition of EGFR signaling can partially rescue the parathyroid hyperplasia phenotype. We propose that because Sema3d is a secreted protein, it may be possible to use recombinant Sema3d or derived peptides to inhibit parathyroid cell proliferation causing hyperplasia and hyperparathyroidism. Collectively, these findings identify Sema3d as a negative regulator of parathyroid growth.
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Affiliation(s)
- Anamika Singh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore 169857
| | - Masum M Mia
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore 169857
| | - Dasan Mary Cibi
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore 169857
| | - Ashutosh Kumar Arya
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Sanjay Kumar Bhadada
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Manvendra K Singh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School Singapore, Singapore 169857; National Heart Research Institute Singapore, National Heart Center Singapore, Singapore 169609.
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14
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Chodur DM, Coulter P, Isaacs J, Pu M, Fernandez N, Waters CM, Rowe-Magnus DA. Environmental Calcium Initiates a Feed-Forward Signaling Circuit That Regulates Biofilm Formation and Rugosity in Vibrio vulnificus. mBio 2018; 9:e01377-18. [PMID: 30154262 DOI: 10.1128/mBio.01377-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The second messenger c-di-GMP is a key regulator of bacterial physiology. The V. vulnificus genome encodes nearly 100 proteins predicted to make, break, and bind c-di-GMP. However, relatively little is known regarding the environmental signals that regulate c-di-GMP levels and biofilm formation in V. vulnificus. Here, we identify calcium as a primary environmental signal that specifically increases intracellular c-di-GMP concentrations, which in turn triggers brp-mediated biofilm formation. We show that PAPS, a metabolic intermediate of the sulfate assimilation pathway, acts as a second messenger linking environmental calcium and sulfur source availability to the production of another intracellular second messenger (c-di-GMP) to regulate biofilm and rugose colony formation, developmental pathways that are associated with environmental persistence and efficient bivalve colonization by this potent human pathogen. Poor clinical outcomes (disfigurement, amputation, and death) and significant economic losses in the aquaculture industry can be attributed to the potent opportunistic human pathogen Vibrio vulnificus. V. vulnificus, as well as the bivalves (oysters) it naturally colonizes, is indigenous to estuaries and human-inhabited coastal regions and must endure constantly changing environmental conditions as freshwater and seawater enter, mix, and exit the water column. Elevated cellular c-di-GMP levels trigger biofilm formation, but relatively little is known regarding the environmental signals that initiate this response. Here, we show that calcium is a primary environmental signal that specifically increases intracellular c-di-GMP concentrations, which in turn triggers expression of the brp extracellular polysaccharide that enhances biofilm formation. A transposon screen for the loss of calcium-induced PbrpA expression revealed CysD, an enzyme in the sulfate assimilation pathway. Targeted disruption of the pathway indicated that the production of a specific metabolic intermediate, 3′-phosphoadenosine 5′-phosphosulfate (PAPS), was required for calcium-induced PbrpA expression and that PAPS was separately required for development of the physiologically distinct rugose phenotype. Thus, PAPS behaves as a second messenger in V. vulnificus. Moreover, c-di-GMP and BrpT (the activator of brp expression) acted in concert to bias expression of the sulfate assimilation pathway toward PAPS and c-di-GMP accumulation, establishing a feed-forward regulatory loop to boost brp expression. Thus, this signaling network links extracellular calcium and sulfur availability to the intracellular second messengers PAPS and c-di-GMP in the regulation of V. vulnificus biofilm formation and rugosity, survival phenotypes underpinning its evolution as a resilient environmental organism.
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Pani AM, Goldstein B. Direct visualization of a native Wnt in vivo reveals that a long-range Wnt gradient forms by extracellular dispersal. eLife 2018; 7:38325. [PMID: 30106379 PMCID: PMC6143344 DOI: 10.7554/elife.38325] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/13/2018] [Indexed: 12/24/2022] Open
Abstract
Wnts are evolutionarily conserved signaling proteins with essential roles in development and disease that have often been thought to spread between cells and signal at a distance. However, recent studies have challenged this model, and whether long-distance extracellular Wnt dispersal occurs and is biologically relevant is debated. Understanding fundamental aspects of Wnt dispersal has been limited by challenges with observing endogenous ligands in vivo, which has prevented directly testing hypotheses. Here, we have generated functional, fluorescently tagged alleles for a C. elegans Wnt homolog and for the first time visualized a native, long-range Wnt gradient in a living animal. Live imaging of Wnt along with source and responding cell membranes provided support for free, extracellular dispersal. By limiting Wnt transfer between cells, we confirmed that extracellular spreading shapes a long-range gradient and is critical for neuroblast migration. These results provide direct evidence that Wnts spread extracellularly to regulate aspects of long-range signaling.
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Affiliation(s)
- Ariel M Pani
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, United States
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina, United States
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16
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State UniversityMansfield, OH, United States
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Lei K, Thi-Kim Vu H, Mohan RD, McKinney SA, Seidel CW, Alexander R, Gotting K, Workman JL, Sánchez Alvarado A. Egf Signaling Directs Neoblast Repopulation by Regulating Asymmetric Cell Division in Planarians. Dev Cell 2016; 38:413-29. [PMID: 27523733 DOI: 10.1016/j.devcel.2016.07.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 06/01/2016] [Accepted: 07/15/2016] [Indexed: 12/27/2022]
Abstract
A large population of proliferative stem cells (neoblasts) is required for physiological tissue homeostasis and post-injury regeneration in planarians. Recent studies indicate that survival of a few neoblasts after sublethal irradiation results in the clonal expansion of the surviving stem cells and the eventual restoration of tissue homeostasis and regenerative capacity. However, the precise mechanisms regulating the population dynamics of neoblasts remain largely unknown. Here, we uncovered a central role for epidermal growth factor (EGF) signaling during in vivo neoblast expansion mediated by Smed-egfr-3 (egfr-3) and its putative ligand Smed-neuregulin-7 (nrg-7). Furthermore, the EGF receptor-3 protein localizes asymmetrically on the cytoplasmic membrane of neoblasts, and the ratio of asymmetric to symmetric cell divisions decreases significantly in egfr-3(RNAi) worms. Our results not only provide the first molecular evidence of asymmetric stem cell divisions in planarians, but also demonstrate that EGF signaling likely functions as an essential regulator of neoblast clonal expansion.
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Affiliation(s)
- Kai Lei
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
| | - Hanh Thi-Kim Vu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ryan D Mohan
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Sean A McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chris W Seidel
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Kirsten Gotting
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
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18
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Abstract
Gas exchange is essential for multicellular organisms. In contrast to the circulatory systems of animals, land plants have tissues with intercellular spaces (ICSs), called aerenchyma, that are critical for efficient gas exchange. Plants form ICSs by two different mechanisms: schizogeny, where localized cell separation creates spaces; and lysogeny, where cells die to create ICSs. In schizogenous ICS formation, specific molecular mechanisms regulate the sites of cell separation and coordinate extensive reorganization of cell walls. Emerging evidence suggests the involvement of extracellular signaling, mediated by peptide ligands and leucine-rich repeat receptor-like kinases, in the regulation of cell wall remodeling during cell separation. Recent work on the liverwort Marchantia polymorpha has demonstrated a critical role for a plasma membrane-associated plant U-box E3 ubiquitin ligase in ICS formation. In this review, I discuss the mechanism of schizogenous ICS formation, focusing on the potential role of extracellular signaling in the regulation of cell separation.
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Pantcheva P, Elias M, Duncan K, Borlongan CV, Tajiri N, Kaneko Y. The role of DJ-1 in the oxidative stress cell death cascade after stroke. Neural Regen Res 2014; 9:1430-3. [PMID: 25317153 PMCID: PMC4192943 DOI: 10.4103/1673-5374.139458] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2014] [Indexed: 12/14/2022] Open
Abstract
Oxidative stress is closely associated with secondary cell death in many disorders of the central nervous system including stroke, Parkinson's disease, Alzheimer's disease. Among many aberrant oxidative stress-associated proteins, DJ-1 has been associated with the oxidative stress cell death cascade primarily in Parkinson's disease. Although principally expressed in the cytoplasm and nucleus, DJ-1 can be secreted into the serum under pathological condition. Recently, a close pathological association between DJ-1 and oxidative stress in stroke has been implicated. To this end, we and others have demonstrated the important role of mitochondria in neuroprotection for stroke by demonstrating that the translocation of DJ-1 in the mitochondria could potentially mitigate mitochondrial injury. Here, we discuss our recent findings testing the hypothesis that DJ-1 not only functions as a form of intracellular protection from oxidative stress, but that it also utilizes paracrine and/or autocrine cues in order to accomplish extracellular signaling between neighboring neuronal cells, resulting in neuroprotection. This article highlights recent evidence supporting the status of DJ-1 as key anti-oxidative stress therapeutic target for stroke.
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Affiliation(s)
- Paolina Pantcheva
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
| | - Maya Elias
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
| | - Kelsey Duncan
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
| | - Cesar V Borlongan
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
| | - Naoki Tajiri
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
| | - Yuji Kaneko
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL, USA
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Mavrici D, Marakalala MJ, Holton JM, Prigozhin DM, Gee CL, Zhang YJ, Rubin EJ, Alber T. Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC. Proc Natl Acad Sci U S A 2014; 111:8037-42. [PMID: 24843173 DOI: 10.1073/pnas.1321812111] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial growth and cell division are coordinated with hydrolysis of the peptidoglycan (PG) layer of the cell wall, but the mechanisms of regulation of extracellular PG hydrolases are not well understood. Here we report the biochemical, structural, and genetic analysis of the Mycobacterium tuberculosis homolog of the transmembrane PG-hydrolase regulator, FtsX. The purified FtsX extracellular domain binds the PG peptidase Rv2190c/RipC N-terminal segment, causing a conformational change that activates the enzyme. Deletion of ftsEX and ripC caused similar phenotypes in Mycobacterium smegmatis, as expected for genes in a single pathway. The crystal structure of the FtsX extracellular domain reveals an unprecedented fold containing two lobes connected by a flexible hinge. Mutations in the hydrophobic cleft between the lobes reduce RipC binding in vitro and inhibit FtsX function in M. smegmatis. These studies suggest how FtsX recognizes RipC and support a model in which a conformational change in FtsX links the cell division apparatus with PG hydrolysis.
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Mobasheri A. Glucose: an energy currency and structural precursor in articular cartilage and bone with emerging roles as an extracellular signaling molecule and metabolic regulator. Front Endocrinol (Lausanne) 2012; 3:153. [PMID: 23251132 PMCID: PMC3523231 DOI: 10.3389/fendo.2012.00153] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 11/19/2012] [Indexed: 01/19/2023] Open
Abstract
In the skeletal system glucose serves as an essential source of energy for the development, growth, and maintenance of bone and articular cartilage. It is particularly needed for skeletal morphogenesis during embryonic growth and fetal development. Glucose is vital for osteogenesis and chondrogenesis, and is used as a precursor for the synthesis of glycosaminoglycans, glycoproteins, and glycolipids. Glucose sensors are present in tissues and organs that carry out bulk glucose fluxes (i.e., intestine, kidney, and liver). The beta cells of the pancreatic islets of Langerhans respond to changes in blood glucose concentration by varying the rate of insulin synthesis and secretion. Neuronal cells in the hypothalamus are also capable of sensing extracellular glucose. Glucosensing neurons use glucose as a signaling molecule to alter their action potential frequency in response to variations in ambient glucose levels. Skeletal muscle and adipose tissue can respond to changes in circulating glucose but much less is known about glucosensing in bone and cartilage. Recent research suggests that bone cells can influence (and be influenced by) systemic glucose metabolism. This focused review article discusses what we know about glucose transport and metabolism in bone and cartilage and highlights recent studies that have linked glucose metabolism, insulin signaling, and osteocalcin activity in bone. These new findings in bone cells raise important questions about nutrient sensing, uptake, storage and processing mechanisms and how they might contribute to overall energy homeostasis in health and disease. The role of glucose in modulating anabolic and catabolic gene expression in normal and osteoarthritic chondrocytes is also discussed. In summary, cartilage and bone cells are sensitive to extracellular glucose and adjust their gene expression and metabolism in response to varying extracellular glucose concentrations.
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Affiliation(s)
- Ali Mobasheri
- *Correspondence: Ali Mobasheri, Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Nottingham, Leicestershire LE12 5RD, UK. e-mail:
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Lobedanz S, Søgaard-Andersen L. Identification of the C-signal, a contact-dependent morphogen coordinating multiple developmental responses in Myxococcus xanthus. Genes Dev 2003; 17:2151-61. [PMID: 12923062 PMCID: PMC196456 DOI: 10.1101/gad.274203] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The regulated accumulation of the contact-dependent extracellular C-signal morphogen in the bacterium Myxococcus xanthus ensures the temporal and spatial coordination of multicellular morphogenesis and cellular differentiation during fruiting body formation. Synthesis of the C-signal depends on the csgA gene. The CsgA protein exists in two forms, the full-length 25-kD protein (p25), which is homologous to short-chain alcohol dehydrogenases, and a 17-kD protein (p17). The molecular nature of the C-signal has remained elusive. Here we show that p25 and p17 are associated with the outer membrane and that p17 copurifies with C-signal activity from M. xanthus cells. p17 corresponds to the C-terminal part of p25. A recombinant p17 protein, which lacks the N-terminal coenzyme binding pocket and which fails to bind NAD+ in vitro, has C-signal activity. These data provide evidence that p17 is the active species in C-signaling and that p17 does not act as a short-chain alcohol dehydrogenase to generate the C-signal. We further provide evidence that p17 is synthesized by N-terminal proteolytic processing of p25 by a serine protease. Compared to other bacterial signaling molecules, p17 is unusual with respect to size and cell-surface association. In these regards, C-signal is functionally analogous to eukaryotic signaling proteins.
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Affiliation(s)
- Sune Lobedanz
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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