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Gavandi T, Patil S, Basrani S, Yankanchi S, Chougule S, Karuppayil SM, Jadhav A. MIG1, TUP1 and NRG1 mediated yeast to hyphal morphogenesis inhibition in Candida albicans by ganciclovir. Braz J Microbiol 2024; 55:2047-2056. [PMID: 38789908 PMCID: PMC11405576 DOI: 10.1007/s42770-024-01344-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024] Open
Abstract
Candida albicans is a polymorphic human fungal pathogen and the prime etiological agent responsible for candidiasis. The main two aspects of C. albicans virulence that have been suggested are yeast-to-hyphal (Y-H) morphological transitions and biofilm development. Anti-fungal agents targeting these virulence attributes enhances the antifungal drug development process. Repositioning with other non-fungal drugs offered a one of the new strategies and a potential alternative option to counter the urgent need for antifungal drug development. In the current study, an antiviral drug ganciclovir was screened as an antifungal agent against ATCC 90028, 10231 and clinical isolate (C1). Ganciclovir at 0.5 mg/ml concentration reduced 50% hyphal development on a silicon-based urinary catheter and was visualized using scanning electron microscopy. Ganciclovir reduced ergosterol biosynthesis in both strains and C1 isolate of C. albicans in a concentration-dependent manner. Additionally, a gene expression profile study showed that ganciclovir treatment resulted in upregulation of hyphal-specific repressors MIG1, TUP1, and NRG1 in C. albicans. Additionally, an in vivo study on the Bombyx mori silkworm model further evidenced the virulence inhibitory ability of ganciclovir (0.5 mg/ml) against C. albicans. This is the first report that explore the novel anti-morphogenic activities of ganciclovir against the pathogenic C. albicans strains, along with clinical isolates. Further, ganciclovir may be considered for therapeutic purpose after combinations with standard antifungal agents.
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Affiliation(s)
- Tanjila Gavandi
- Department of Stem cell and Regenerative Medicine, Medical Biotechnology, Centre for Interdisciplinary Research, D. Y. Patil Education Society (Deemed to be University), 416006, Kolhapur, Maharashtra, India
| | - Shivani Patil
- Department of Stem cell and Regenerative Medicine, Medical Biotechnology, Centre for Interdisciplinary Research, D. Y. Patil Education Society (Deemed to be University), 416006, Kolhapur, Maharashtra, India
| | - Sargun Basrani
- Department of Stem cell and Regenerative Medicine, Medical Biotechnology, Centre for Interdisciplinary Research, D. Y. Patil Education Society (Deemed to be University), 416006, Kolhapur, Maharashtra, India
| | - Shivanand Yankanchi
- Department of Zoology, Shivaji University, Vidya Nagar, 416004, Kolhapur, Maharashtra, India
| | - Sayali Chougule
- Department of Stem cell and Regenerative Medicine, Medical Biotechnology, Centre for Interdisciplinary Research, D. Y. Patil Education Society (Deemed to be University), 416006, Kolhapur, Maharashtra, India
| | - S Mohan Karuppayil
- Department of Stem cell and Regenerative Medicine, Medical Biotechnology, Centre for Interdisciplinary Research, D. Y. Patil Education Society (Deemed to be University), 416006, Kolhapur, Maharashtra, India.
| | - Ashwini Jadhav
- Department of Stem cell and Regenerative Medicine, Medical Biotechnology, Centre for Interdisciplinary Research, D. Y. Patil Education Society (Deemed to be University), 416006, Kolhapur, Maharashtra, India.
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2
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Chen L, Weir JR. The molecular machinery of meiotic recombination. Biochem Soc Trans 2024; 52:379-393. [PMID: 38348856 PMCID: PMC10903461 DOI: 10.1042/bst20230712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Meiotic recombination, a cornerstone of eukaryotic diversity and individual genetic identity, is essential for the creation of physical linkages between homologous chromosomes, facilitating their faithful segregation during meiosis I. This process requires that germ cells generate controlled DNA lesions within their own genome that are subsequently repaired in a specialised manner. Repair of these DNA breaks involves the modulation of existing homologous recombination repair pathways to generate crossovers between homologous chromosomes. Decades of genetic and cytological studies have identified a multitude of factors that are involved in meiotic recombination. Recent work has started to provide additional mechanistic insights into how these factors interact with one another, with DNA, and provide the molecular outcomes required for a successful meiosis. Here, we provide a review of the recent developments with a focus on protein structures and protein-protein interactions.
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Affiliation(s)
- Linda Chen
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - John R. Weir
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory, Max-Planck-Ring 9, 72076 Tübingen, Germany
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Rodriguez Gallo MC, Uhrig RG. Phosphorylation mediated regulation of RNA splicing in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1249057. [PMID: 37780493 PMCID: PMC10539000 DOI: 10.3389/fpls.2023.1249057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023]
Abstract
For the past two decades, the study of alternative splicing (AS) and its involvement in plant development and stress response has grown in popularity. Only recently however, has the focus shifted to the study of how AS regulation (or lack-thereof) affects downstream mRNA and protein landscapes and how these AS regulatory events impact plant development and stress tolerance. In humans, protein phosphorylation represents one of the predominant mechanisms by which AS is regulated and thus the protein kinases governing these phosphorylation events are of interest for further study. Large-scale phosphoproteomic studies in plants have consistently found that RNA splicing-related proteins are extensively phosphorylated, however, the signaling pathways involved in AS regulation have not been resolved. In this mini-review, we summarize our current knowledge of the three major splicing-related protein kinase families in plants that are suggested to mediate AS phospho-regulation and draw comparisons to their metazoan orthologs. We also summarize and contextualize the phosphorylation events identified as occurring on splicing-related protein families to illustrate the high degree to which splicing-related proteins are modified, placing a new focus on elucidating the impacts of AS at the protein and PTM-level.
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Affiliation(s)
| | - R. Glen Uhrig
- University of Alberta, Department of Biological Sciences, Edmonton, AB, Canada
- University of Alberta, Department of Biochemistry, Edmonton, AB, Canada
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4
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Jafari NV, Rohn JL. An immunoresponsive three-dimensional urine-tolerant human urothelial model to study urinary tract infection. Front Cell Infect Microbiol 2023; 13:1128132. [PMID: 37051302 PMCID: PMC10083561 DOI: 10.3389/fcimb.2023.1128132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/01/2023] [Indexed: 03/29/2023] Open
Abstract
IntroductionMurine models of urinary tract infection (UTI) have improved our understanding of host-pathogen interactions. However, given differences between rodent and human bladders which may modulate host and bacterial response, including certain biomarkers, urothelial thickness and the concentration of urine, the development of new human-based models is important to complement mouse studies and to provide a more complete picture of UTI in patients.MethodsWe originally developed a human urothelial three-dimensional (3D) model which was urine tolerant and demonstrated several urothelial biomarkers, but it only achieved human thickness in heterogenous, multi-layered zones and did not demonstrate the comprehensive differentiation status needed to achieve barrier function. We optimised this model by altering a variety of conditions and validated it with microscopy, flow cytometry, transepithelial electrical resistance and FITC-dextran permeability assays to confirm tissue architecture, barrier integrity and response to bacterial infection.ResultsWe achieved an improved 3D urine-tolerant human urothelial model (3D-UHU), which after 18-20 days of growth, stratified uniformly to 7-8 layers comprised of the three expected, distinct human cell types. The apical surface differentiated into large, CD227+ umbrella-like cells expressing uroplakin-1A, II, III, and cytokeratin 20, all of which are important terminal differentiation markers, and a glycosaminoglycan layer. Below this layer, several layers of intermediate cells were present, with a single underlying layer of CD271+ basal cells. The apical surface also expressed E-cadherin, ZO-1, claudin-1 and -3, and the model possessed good barrier function. Infection with both Gram-negative and Gram-positive bacterial classes elicited elevated levels of pro-inflammatory cytokines and chemokines characteristic of urinary tract infection in humans and caused a decrease in barrier function.DiscussionTaken together, 3D-UHU holds promise for studying host-pathogen interactions and host urothelial immune response.
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Mo D, Xu S, Rosa JP, Hasan S, Adams W. Dynamic Python-Based Method Provides Quantitative Analysis of Intercellular Junction Organization During S. pneumoniae Infection of the Respiratory Epithelium. Front Cell Infect Microbiol 2022; 12:865528. [PMID: 35755841 PMCID: PMC9230243 DOI: 10.3389/fcimb.2022.865528] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/30/2022] [Indexed: 12/11/2022] Open
Abstract
Many respiratory pathogens compromise epithelial barrier function during lung infection by disrupting intercellular junctions, such as adherens junctions and tight junctions, that maintain intercellular integrity. This includes Streptococcus pneumoniae, a leading cause of pneumonia, which can successfully breach the epithelial barrier and cause severe infections such as septicemia and meningitis. Fluorescence microscopy analysis on intercellular junction protein manipulation by respiratory pathogens has yielded major advances in our understanding of their pathogenesis. Unfortunately, a lack of automated image analysis tools that can tolerate variability in sample-sample staining has limited the accuracy in evaluating intercellular junction organization quantitatively. We have created an open source, automated Python computer script called "Intercellular Junction Organization Quantification" or IJOQ that can handle a high degree of sample-sample staining variability and robustly measure intercellular junction integrity. In silico validation of IJOQ was successful in analyzing computer generated images containing varying degrees of simulated intercellular junction disruption. Accurate IJOQ analysis was further confirmed using images generated from in vitro and in vivo bacterial infection models. When compared in parallel to a previously published, semi-automated script used to measure intercellular junction organization, IJOQ demonstrated superior analysis for all in vitro and in vivo experiments described herein. These data indicate that IJOQ is an unbiased, easy-to-use tool for fluorescence microscopy analysis and will serve as a valuable, automated resource to rapidly quantify intercellular junction disruption under diverse experimental conditions.
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Affiliation(s)
- Devons Mo
- Department of Biological Sciences, San Jose State University, San Jose, CA, United States
| | - Shuying Xu
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, United States,Graduate Program in Immunology, Tufts Graduate School of Biomedical Sciences, Boston, MA, United States
| | - Juan P. Rosa
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, United States,Graduate Program in Immunology, Tufts Graduate School of Biomedical Sciences, Boston, MA, United States,Department of Biology, University of Puerto Rico, Cayey, PR, United States
| | - Shakir Hasan
- Institute of Microbiology of the CAS, Prague, Czechia
| | - Walter Adams
- Department of Biological Sciences, San Jose State University, San Jose, CA, United States,*Correspondence: Walter Adams,
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Naro C, Barbagallo F, Caggiano C, De Musso M, Panzeri V, Di Agostino S, Paronetto MP, Sette C. Functional Interaction Between the Oncogenic Kinase NEK2 and Sam68 Promotes a Splicing Program Involved in Migration and Invasion in Triple-Negative Breast Cancer. Front Oncol 2022; 12:880654. [PMID: 35530315 PMCID: PMC9068942 DOI: 10.3389/fonc.2022.880654] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/16/2022] [Indexed: 12/01/2022] Open
Abstract
Triple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype. Poor prognosis in TNBC is partly due to lack of efficacious targeted therapy and high propensity to metastasize. Dysregulation of alternative splicing has recently emerged as a trait of TNBC, suggesting that unveiling the molecular mechanisms underlying its regulation could uncover new druggable cancer vulnerabilities. The oncogenic kinase NEK2 is significantly upregulated in TNBC and contributes to shaping their unique splicing profile. Herein, we found that NEK2 interacts with the RNA binding protein Sam68 in TNBC cells and that NEK2-mediated phosphorylation of Sam68 enhances its splicing activity. Genome-wide transcriptome analyses identified the splicing targets of Sam68 in TNBC cells and revealed a common set of exons that are co-regulated by NEK2. Functional annotation of splicing-regulated genes highlighted cell migration and spreading as biological processes regulated by Sam68. Accordingly, Sam68 depletion reduces TNBC cell migration and invasion, and these effects are potentiated by the concomitant inhibition of NEK2 activity. Our findings indicate that Sam68 and NEK2 functionally cooperate in the regulation of a splicing program that sustains the pro-metastatic features of TNBC cells.
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Affiliation(s)
- Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy.,Gemelli SCIENCE and TECHNOLOGY PARK (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Federica Barbagallo
- Department of Experimental Medicine, University of Rome Sapienza, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy.,Gemelli SCIENCE and TECHNOLOGY PARK (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Monica De Musso
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy
| | - Valentina Panzeri
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy.,Gemelli SCIENCE and TECHNOLOGY PARK (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Silvia Di Agostino
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Rome, Italy.,Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, University of the Sacred Hearth, Rome, Italy.,Gemelli SCIENCE and TECHNOLOGY PARK (GSTeP)-Organoids Research Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
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7
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Nasuno R, Suzuki S, Oiki S, Hagiwara D, Takagi H. Identification and Functional Analysis of GTP Cyclohydrolase II in Candida glabrata in Response to Nitrosative Stress. Front Microbiol 2022; 13:825121. [PMID: 35308400 PMCID: PMC8924521 DOI: 10.3389/fmicb.2022.825121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/14/2022] [Indexed: 11/18/2022] Open
Abstract
Reactive nitrogen species (RNS) are signal molecules involved in various biological events; however, excess levels of RNS cause nitrosative stress, leading to cell death and/or cellular dysfunction. During the process of infection, pathogens are exposed to nitrosative stress induced by host-derived RNS. Therefore, the nitrosative stress resistance mechanisms of pathogenic microorganisms are important for their infection and pathogenicity, and could be promising targets for antibiotics. Previously, we demonstrated that the RIB1 gene encoding GTP cyclohydrolase II (GCH2), which catalyzes the first step of the riboflavin biosynthesis pathway, is important for nitrosative stress resistance in the yeast Saccharomyces cerevisiae. Here, we identified and characterized the RIB1 gene in the opportunistic pathogenic yeast Candida glabrata. Our genetic and biochemical analyses indicated that the open reading frame of CAGL0F04279g functions as RIB1 in C. glabrata (CgRIB1). Subsequently, we analyzed the effect of CgRIB1 on nitrosative stress resistance by a growth test in the presence of RNS. Overexpression or deletion of CgRIB1 increased or decreased the nitrosative stress resistance of C. glabrata, respectively, indicating that GCH2 confers nitrosative stress resistance on yeast cells. Moreover, we showed that the proliferation of C. glabrata in cultures of macrophage-like cells required the GCH2-dependent nitrosative stress detoxifying mechanism. Additionally, an infection assay using silkworms as model host organisms indicated that CgRIB1 is indispensable for the virulence of C. glabrata. Our findings suggest that the GCH2-dependent nitrosative stress detoxifying mechanism is a promising target for the development of novel antibiotics.
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Affiliation(s)
- Ryo Nasuno
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Soma Suzuki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Sayoko Oiki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Daisuke Hagiwara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
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Carmichael RE, Schrader M. Determinants of Peroxisome Membrane Dynamics. Front Physiol 2022; 13:834411. [PMID: 35185625 PMCID: PMC8853631 DOI: 10.3389/fphys.2022.834411] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Organelles within the cell are highly dynamic entities, requiring dramatic morphological changes to support their function and maintenance. As a result, organelle membranes are also highly dynamic, adapting to a range of topologies as the organelle changes shape. In particular, peroxisomes—small, ubiquitous organelles involved in lipid metabolism and reactive oxygen species homeostasis—display a striking plasticity, for example, during the growth and division process by which they proliferate. During this process, the membrane of an existing peroxisome elongates to form a tubule, which then constricts and ultimately undergoes scission to generate new peroxisomes. Dysfunction of this plasticity leads to diseases with developmental and neurological phenotypes, highlighting the importance of peroxisome dynamics for healthy cell function. What controls the dynamics of peroxisomal membranes, and how this influences the dynamics of the peroxisomes themselves, is just beginning to be understood. In this review, we consider how the composition, biophysical properties, and protein-lipid interactions of peroxisomal membranes impacts on their dynamics, and in turn on the biogenesis and function of peroxisomes. In particular, we focus on the effect of the peroxin PEX11 on the peroxisome membrane, and its function as a major regulator of growth and division. Understanding the roles and regulation of peroxisomal membrane dynamics necessitates a multidisciplinary approach, encompassing knowledge across a range of model species and a number of fields including lipid biochemistry, biophysics and computational biology. Here, we present an integrated overview of our current understanding of the determinants of peroxisome membrane dynamics, and reflect on the outstanding questions still remaining to be solved.
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Affiliation(s)
- Ruth E Carmichael
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
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9
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Gallego-Jara J, Ortega Á, Lozano Terol G, Sola Martínez RA, Cánovas Díaz M, de Diego Puente T. Bacterial Sirtuins Overview: An Open Niche to Explore. Front Microbiol 2021; 12:744416. [PMID: 34803965 PMCID: PMC8603916 DOI: 10.3389/fmicb.2021.744416] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Sirtuins are deacetylase enzymes widely distributed in all domains of life. Although for decades they have been related only to histones deacetylation in eukaryotic organisms, today they are considered global regulators in both prokaryotes and eukaryotes. Despite the important role of sirtuins in humans, the knowledge about bacterial sirtuins is still limited. Several proteomics studies have shown that bacterial sirtuins deacetylate a large number of lysines in vivo, although the effect that this deacetylation causes in most of them remains unknown. To date, only the regulation of a few bacterial sirtuin substrates has been characterized, being their metabolic roles widely distributed: carbon and nitrogen metabolism, DNA transcription, protein translation, or virulence. One of the most current topics on acetylation and deacetylation focuses on studying stoichiometry using quantitative LC-MS/MS. The results suggest that prokaryotic sirtuins deacetylate at low stoichiometry sites, although more studies are needed to know if it is a common characteristic of bacterial sirtuins and its biological significance. Unlike eukaryotic organisms, bacteria usually have one or few sirtuins, which have been reported to have closer phylogenetic similarity with the human Sirt5 than with any other human sirtuin. In this work, in addition to carrying out an in-depth review of the role of bacterial sirtuins in their physiology, a phylogenetic study has been performed that reveals the evolutionary differences between sirtuins of different bacterial species and even between homologous sirtuins.
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Affiliation(s)
- Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Gema Lozano Terol
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Rosa A Sola Martínez
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
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10
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Fokin AI, Gautreau AM. Assembly and Activity of the WASH Molecular Machine: Distinctive Features at the Crossroads of the Actin and Microtubule Cytoskeletons. Front Cell Dev Biol 2021; 9:658865. [PMID: 33869225 PMCID: PMC8047104 DOI: 10.3389/fcell.2021.658865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/12/2021] [Indexed: 01/10/2023] Open
Abstract
The Arp2/3 complex generates branched actin networks at different locations of the cell. The WASH and WAVE Nucleation Promoting Factors (NPFs) activate the Arp2/3 complex at the surface of endosomes or at the cell cortex, respectively. In this review, we will discuss how these two NPFs are controlled within distinct, yet related, multiprotein complexes. These complexes are not spontaneously assembled around WASH and WAVE, but require cellular assembly factors. The centrosome, which nucleates microtubules and branched actin, appears to be a privileged site for WASH complex assembly. The actin and microtubule cytoskeletons are both responsible for endosome shape and membrane remodeling. Motors, such as dynein, pull endosomes and extend membrane tubules along microtubule tracks, whereas branched actin pushes onto the endosomal membrane. It was recently uncovered that WASH assembles a super complex with dynactin, the major dynein activator, where the Capping Protein (CP) is exchanged from dynactin to the WASH complex. This CP swap initiates the first actin filament that primes the autocatalytic nucleation of branched actin at the surface of endosomes. Possible coordination between pushing and pulling forces in the remodeling of endosomal membranes is discussed.
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Affiliation(s)
- Artem I. Fokin
- Laboratoire de Biologie Structurale de la Cellule, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Alexis M. Gautreau
- Laboratoire de Biologie Structurale de la Cellule, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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11
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Olajide OJ, Gbadamosi IT, Yawson EO, Arogundade T, Lewu FS, Ogunrinola KY, Adigun OO, Bamisi O, Lambe E, Arietarhire LO, Oluyomi OO, Idowu OK, Kareem R, Asogwa NT, Adeniyi PA. Hippocampal Degeneration and Behavioral Impairment During Alzheimer-Like Pathogenesis Involves Glutamate Excitotoxicity. J Mol Neurosci 2021; 71:1205-1220. [PMID: 33420680 DOI: 10.1007/s12031-020-01747-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022]
Abstract
The hallmarks of Alzheimer's disease (AD) pathology include senile plaques accumulation and neurofibrillary tangles, which is thought to underlie synaptic failure. Recent evidence however supports that synaptic failure in AD may instead be instigated by enhanced N-methyl-D-aspartate (NMDA) activity, via a reciprocal relationship between soluble amyloid-β (Aβ) accumulation and increased glutamate agonist. While previous studies have shown Aβ-mediated alterations to the glutamatergic system during AD, the underlying etiology of excitotoxic glutamate-induced changes has not been explored. Here, we investigated the acute effects of stereotaxic dentate gyrus (DG) glutamate injection on behavior and molecular expression of specific proteins and neurochemicals modulating hippocampal functions. Dependence of glutamate-mediated effects on NMDA receptor (NMDAR) hyperactivation was tested using NMDARs antagonist memantine. DG of Wistar rats (12-weeks-old) were bilaterally microinjected with glutamate (500 mM) with or without daily intraperitoneal (i.p.) memantine injection (20 mg/kg) for 14 days, while controls received either intrahippocampal/i.p. PBS or i.p. memantine. Behavioral characterization in open field and Y-maze revealed that glutamate evoked anxiogenic responses and perturbed spatial memory were inhibited by memantine. In glutamate-treated rats, increased NO expression was accompanied by marked reduction in profiles of glutathione-s-transferase and glutathione peroxidase. Similarly, glutamate-mediated increase in acetylcholinesterase expression corroborated downregulation of synaptophysin and PSD-95, coupled with initiation of reactive astrogliosis (GFAP). While neurofilament immunolocalization/immunoexpression was unperturbed, we found glutamate-mediated reduction in neurogenic markers Ki67 and PCNA immunoexpression, with a decrease in NR2B protein expression, whereas mGluR1 remains unchanged. In addition, increased expression of apoptotic regulatory proteins p53 and Bax was seen in glutamate infused rats, corroborating chromatolytic degeneration of granule neurons in the DG. Interestingly, memantine abrogated most of the degenerative changes associated with glutamate excitotoxicity in this study. Taken together, our findings causally link acute glutamate dyshomeostasis in the DG with development of AD-related behavioral impairment and molecular neurodegeneration.
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Affiliation(s)
- Olayemi Joseph Olajide
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria. .,Center for Studies in Behavioral Neurobiology, Department of Psychology, Concordia University, Montreal, Canada.
| | - Ismail Tayo Gbadamosi
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.,Central Research Laboratories Ltd, 132b University Road, Ilorin, Nigeria
| | - Emmanuel Olusola Yawson
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.,Department of Anatomy, Faculty of Basic Medical Sciences, Redeemer's University, Ede, Nigeria
| | - Tolulope Arogundade
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.,Department of Anatomy, Faculty of Basic Medical Sciences, Adeleke University, Ede, Nigeria
| | - Folashade Susan Lewu
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Kehinde Yomi Ogunrinola
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.,Department of Anatomy, School of Post-Basic Nursing, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Oluwaseun Olaniyi Adigun
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Olawande Bamisi
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.,Department of Anatomy, Faculty of Basic Medical Sciences, Ekiti State University, Ado Ekiti, Nigeria
| | - Ezra Lambe
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Leviticus Ogbenevurinrin Arietarhire
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Olushola Oladapo Oluyomi
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Olumayowa Kolawole Idowu
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Rukayat Kareem
- Department of Anatomy, Division of Neurobiology, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Nnaemeka Tobechukwu Asogwa
- Central Research Laboratories Ltd, 132b University Road, Ilorin, Nigeria.,Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria
| | - Philip Adeyemi Adeniyi
- Department of Comparative Biomedical Sciences, Louisiana State University, Baton Rouge, LA, USA
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12
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Azadi AS, Carmichael RE, Kovacs WJ, Koster J, Kors S, Waterham HR, Schrader M. A Functional SMAD2/3 Binding Site in the PEX11β Promoter Identifies a Role for TGFβ in Peroxisome Proliferation in Humans. Front Cell Dev Biol 2020; 8:577637. [PMID: 33195217 PMCID: PMC7644849 DOI: 10.3389/fcell.2020.577637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/01/2020] [Indexed: 01/10/2023] Open
Abstract
In mammals, peroxisomes perform crucial functions in cellular metabolism, signaling and viral defense which are essential to the viability of the organism. Molecular cues triggered by changes in the cellular environment induce a dynamic response in peroxisomes, which manifests itself as a change in peroxisome number, altered enzyme levels and adaptations to the peroxisomal morphology. How the regulation of this process is integrated into the cell's response to different stimuli, including the signaling pathways and factors involved, remains unclear. Here, a cell-based peroxisome proliferation assay has been applied to investigate the ability of different stimuli to induce peroxisome proliferation. We determined that serum stimulation, long-chain fatty acid supplementation and TGFβ application all increase peroxisome elongation, a prerequisite for proliferation. Time-resolved mRNA expression during the peroxisome proliferation cycle revealed a number of peroxins whose expression correlated with peroxisome elongation, including the β isoform of PEX11, but not the α or γ isoforms. An initial map of putative regulatory motif sites in the respective promoters showed a difference between binding sites in PEX11α and PEX11β, suggesting that these genes may be regulated by distinct pathways. A functional SMAD2/3 binding site in PEX11β points to the involvement of the TGFβ signaling pathway in expression of this gene and thus peroxisome proliferation/dynamics in humans.
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Affiliation(s)
- Afsoon S Azadi
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ruth E Carmichael
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Werner J Kovacs
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology in Zürich (ETH Zürich), Zurich, Switzerland
| | - Janet Koster
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, Netherlands
| | - Suzan Kors
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, Netherlands
| | - Michael Schrader
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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13
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Bostock MP, Prasad AR, Chaouni R, Yuen AC, Sousa-Nunes R, Amoyel M, Fernandes VM. An Immobilization Technique for Long-Term Time-Lapse Imaging of Explanted Drosophila Tissues. Front Cell Dev Biol 2020; 8:590094. [PMID: 33117817 PMCID: PMC7576353 DOI: 10.3389/fcell.2020.590094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/15/2020] [Indexed: 01/19/2023] Open
Abstract
Time-lapse imaging is an essential tool to study dynamic biological processes that cannot be discerned from fixed samples alone. However, imaging cell- and tissue-level processes in intact animals poses numerous challenges if the organism is opaque and/or motile. Explant cultures of intact tissues circumvent some of these challenges, but sample drift remains a considerable obstacle. We employed a simple yet effective technique to immobilize tissues in medium-bathed agarose. We applied this technique to study multiple Drosophila tissues from first-instar larvae to adult stages in various orientations and with no evidence of anisotropic pressure or stress damage. Using this method, we were able to image fine features for up to 18 h and make novel observations. Specifically, we report that fibers characteristic of quiescent neuroblasts are inherited by their basal daughters during reactivation; that the lamina in the developing visual system is assembled roughly 2-3 columns at a time; that lamina glia positions are dynamic during development; and that the nuclear envelopes of adult testis cyst stem cells do not break down completely during mitosis. In all, we demonstrate that our protocol is well-suited for tissue immobilization and long-term live imaging, enabling new insights into tissue and cell dynamics in Drosophila.
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Affiliation(s)
- Matthew P. Bostock
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Anadika R. Prasad
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Rita Chaouni
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Alice C. Yuen
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Rita Sousa-Nunes
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Vilaiwan M. Fernandes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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14
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Soto-Avellaneda A, Morrison BE. Signaling and other functions of lipids in autophagy: a review. Lipids Health Dis 2020; 19:214. [PMID: 32998777 PMCID: PMC7525950 DOI: 10.1186/s12944-020-01389-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
The process of autophagy is integral to cellular function. In this process, proteins, organelles, and metabolites are engulfed in a lipid vesicle and trafficked to a lysosome for degradation. Its central role in protein and organelle homeostasis has piqued interest for autophagy dysfunction as a driver of pathology for a number of diseases including cancer, muscular disorders, neurological disorders, and non-alcoholic fatty liver disease. For much of its history, the study of autophagy has centered around proteins, however, due to advances in mass spectrometry and refined methodologies, the role of lipids in this essential cellular process has become more apparent. This review discusses the diverse endogenous lipid compounds shown to mediate autophagy. Downstream lipid signaling pathways are also reviewed in the context of autophagy regulation. Specific focus is placed upon the Mammalian Target of Rapamycin (mTOR) and Peroxisome Proliferator-Activated Receptor (PPAR) signaling pathways as integration hubs for lipid regulation of autophagy.
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Affiliation(s)
| | - Brad E Morrison
- Biomolecular Sciences Graduate programs, Boise State University, Boise, ID, 83725, USA.
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA.
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15
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Adriaens C, Rambow F, Bervoets G, Silla T, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S, Jensen TH, Marine JC. The long noncoding RNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth. RNA (NEW YORK, N.Y.) 2019; 25:1681-1695. [PMID: 31551298 PMCID: PMC6859857 DOI: 10.1261/rna.071456.119] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/30/2019] [Indexed: 05/27/2023]
Abstract
NEAT1 is one of the most studied lncRNAs, in part because its silencing in mice causes defects in mammary gland development and corpus luteum formation and protects them from skin cancer development. Moreover, depleting NEAT1 in established cancer cell lines reduces growth and sensitizes cells to DNA damaging agents. However, NEAT1 produces two isoforms and because the short isoform, NEAT1_1, completely overlaps the 5' part of the long NEAT1_2 isoform; the respective contributions of each of the isoforms to these phenotypes has remained unclear. Whereas NEAT1_1 is highly expressed in most tissues, NEAT1_2 is the central architectural component of paraspeckles, which are nuclear bodies that assemble in specific tissues and cells exposed to various forms of stress. Using dual RNA-FISH to detect both NEAT1_1 outside of the paraspeckles and NEAT1_2/NEAT1 inside this nuclear body, we report herein that NEAT1_1 levels are dynamically regulated during the cell cycle and targeted for degradation by the nuclear RNA exosome. Unexpectedly, however, cancer cells engineered to lack NEAT1_1, but not NEAT1_2, do not exhibit cell cycle defects. Moreover, Neat1_1-specific knockout mice do not exhibit the phenotypes observed in Neat1-deficient mice. We propose that NEAT1 functions are mainly, if not exclusively, attributable to NEAT1_2 and, by extension, to paraspeckles.
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Affiliation(s)
- Carmen Adriaens
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Toomas Silla
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, 351-0198 Saitama, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 113-8510 Tokyo, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 113-8510 Tokyo, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, 060-0808 Sapporo, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, 060-0812 Sapporo, Japan
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
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16
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Gaete-Argel A, Márquez CL, Barriga GP, Soto-Rifo R, Valiente-Echeverría F. Strategies for Success. Viral Infections and Membraneless Organelles. Front Cell Infect Microbiol 2019; 9:336. [PMID: 31681621 PMCID: PMC6797609 DOI: 10.3389/fcimb.2019.00336] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
Regulation of RNA homeostasis or “RNAstasis” is a central step in eukaryotic gene expression. From transcription to decay, cellular messenger RNAs (mRNAs) associate with specific proteins in order to regulate their entire cycle, including mRNA localization, translation and degradation, among others. The best characterized of such RNA-protein complexes, today named membraneless organelles, are Stress Granules (SGs) and Processing Bodies (PBs) which are involved in RNA storage and RNA decay/storage, respectively. Given that SGs and PBs are generally associated with repression of gene expression, viruses have evolved different mechanisms to counteract their assembly or to use them in their favor to successfully replicate within the host environment. In this review we summarize the current knowledge about the viral regulation of SGs and PBs, which could be a potential novel target for the development of broad-spectrum antiviral therapies.
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Affiliation(s)
- Aracelly Gaete-Argel
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Chantal L Márquez
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Gonzalo P Barriga
- Emerging Viruses Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Molecular and Cellular Virology Laboratory, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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17
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Costello JL, Passmore JB, Islinger M, Schrader M. Multi-localized Proteins: The Peroxisome-Mitochondria Connection. Subcell Biochem 2019; 89:383-415. [PMID: 30378033 DOI: 10.1007/978-981-13-2233-4_17] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Peroxisomes and mitochondria are dynamic, multifunctional organelles that play pivotal cooperative roles in the metabolism of cellular lipids and reactive oxygen species. Their functional interplay, the "peroxisome-mitochondria connection", also includes cooperation in anti-viral signalling and defence, as well as coordinated biogenesis by sharing key division proteins. In this review, we focus on multi-localised proteins which are shared by peroxisomes and mitochondria in mammals. We first outline the targeting and sharing of matrix proteins which are involved in metabolic cooperation. Next, we discuss shared components of peroxisomal and mitochondrial dynamics and division, and we present novel insights into the dual targeting of tail-anchored membrane proteins. Finally, we provide an overview of what is currently known about the role of shared membrane proteins in disease. What emerges is that sharing of proteins between these two organelles plays a key role in their cooperative functions which, based on new findings, may be more extensive than originally envisaged. Gaining a better insight into organelle interplay and the targeting of shared proteins is pivotal to understanding how organelle cooperation contributes to human health and disease.
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Affiliation(s)
| | | | - Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine & Medical Technology Mannheim, Medical Faculty Manheim, University of Heidelberg, 68167, Mannheim, Germany
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18
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The association of dietary animal and plant protein with putative risk markers of colorectal cancer in overweight pre-diabetic individuals during a weight-reducing programme: a PREVIEW sub-study. Eur J Nutr 2019; 59:1517-1527. [PMID: 31139889 DOI: 10.1007/s00394-019-02008-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/21/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE Diets with increased protein content are popular strategies for body weight regulation, but the effect of such diets for the colonic luminal environment is unclear. We aimed to investigate the associations between putative colorectal cancer-related markers and total protein intake, plant and animal proteins, and protein from red and processed meat in pre-diabetic adults (> 25 years). METHODS Analyses were based on clinical and dietary assessments at baseline and after 1 year of intervention. Protein intake was assessed from 4-day dietary records. Putative colorectal cancer-related markers identified from 24-h faecal samples collected over three consecutive days were: concentration of short-chain fatty acids, phenols, ammonia, and pH. RESULTS In total, 79 participants were included in the analyses. We found a positive association between change in total protein intake (slope: 74.72 ± 28.84 µmol per g faeces/E%, p = 0.01), including animal protein intake (slope: 87.63 ± 32.04 µmol per g faeces/E%, p = 0.009), and change in faecal ammonia concentration. For change in ammonia, there was a dose-response trend from the most negative (lowest tertile) to the most positive (highest tertile) association (p = 0.01): in the high tertile, a change in intake of red meat was positively associated with an increase in ammonia excretion (slope: 2.0 ± 0.5 µmol per g faeces/g/day, p < 0.001), whereas no such association was found in the low and medium tertile groups. CONCLUSION Increases in total and animal protein intakes were associated with higher excretion of ammonia in faeces after 1 year in overweight pre-diabetic adults undertaking a weight-loss intervention. An increase in total or relative protein intake, or in the ratio of animal to plant protein, was not associated with an increase in faeces of any of the other putative colorectal cancer risk markers. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT01777893.
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19
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Abstract
Peroxisomes are key metabolic organelles, which contribute to cellular lipid metabolism, e.g. the β-oxidation of fatty acids and the synthesis of myelin sheath lipids, as well as cellular redox balance. Peroxisomal dysfunction has been linked to severe metabolic disorders in man, but peroxisomes are now also recognized as protective organelles with a wider significance in human health and potential impact on a large number of globally important human diseases such as neurodegeneration, obesity, cancer, and age-related disorders. Therefore, the interest in peroxisomes and their physiological functions has significantly increased in recent years. In this review, we intend to highlight recent discoveries, advancements and trends in peroxisome research, and present an update as well as a continuation of two former review articles addressing the unsolved mysteries of this astonishing organelle. We summarize novel findings on the biological functions of peroxisomes, their biogenesis, formation, membrane dynamics and division, as well as on peroxisome-organelle contacts and cooperation. Furthermore, novel peroxisomal proteins and machineries at the peroxisomal membrane are discussed. Finally, we address recent findings on the role of peroxisomes in the brain, in neurological disorders, and in the development of cancer.
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Affiliation(s)
- Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, Medical Faculty Manheim, University of Heidelberg, 68167, Mannheim, Germany
| | - Alfred Voelkl
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany
| | - H Dariush Fahimi
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany
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20
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du Plessis M, Franken J, Bauer FF. Carnitine Requires Choline to Exert Physiological Effects in Saccharomyces cerevisiae. Front Microbiol 2018; 9:1362. [PMID: 30034373 PMCID: PMC6043790 DOI: 10.3389/fmicb.2018.01362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/05/2018] [Indexed: 11/25/2022] Open
Abstract
L-Carnitine is a key metabolite in the energy metabolism of eukaryotic cells, functioning as a shuttling molecule for activated acyl-residues between cellular compartments. In higher eukaryotes this function is essential, and defects in carnitine metabolism has severe effects on fatty acid and carbon metabolism. Carnitine supplementation has been associated with an array of mostly beneficial impacts in higher eukaryotic cells, including stress protection and regulation of redox metabolism in diseased cells. Some of these phenotypes have no obvious link to the carnitine shuttle, and suggest that carnitine has as yet unknown shuttle-independent functions. The existence of shuttle-independent functions has also been suggested in Saccharomyces cerevisiae, including a beneficial effect during hydrogen peroxide stress and a detrimental impact when carnitine is co-supplemented with the reducing agent dithiothreitol (DTT). Here we used these two distinct yeast phenotypes to screen for potential genetic factors that suppress the shuttle independent physiological effects of carnitine. Two deletion strains, Δcho2 and Δopi3, coding for enzymes that catalyze the sequential conversion of phosphatidylethanolamine to phosphatidylcholine were identified for suppressing the phenotypic effects of carnitine. Additional characterisation indicated that the suppression cannot be explained by differences in phospholipid homeostasis. The phenotypes could be reinstated by addition of extracellular choline, but show that the requirement for choline is not based on some overlapping function or the structural similarities of the two molecules. This is the first study to suggest a molecular link between a specific metabolite and carnitine-dependent, but shuttle-independent phenotypes in eukaryotes.
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Affiliation(s)
| | | | - Florian F. Bauer
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch University, Stellenbosch, South Africa
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21
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Catinean A, Neag MA, Muntean DM, Bocsan IC, Buzoianu AD. An overview on the interplay between nutraceuticals and gut microbiota. PeerJ 2018; 6:e4465. [PMID: 29576949 PMCID: PMC5855885 DOI: 10.7717/peerj.4465] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/15/2018] [Indexed: 12/26/2022] Open
Abstract
Background Nowadays, growing attention was being given to the alternative ways to prevent or treat diseases. Nutraceuticals are used increasingly for this purpose. Many of these are being used as alternative therapy. Classic therapy with synthetic drugs, although very effective, has many side effects. The term “nutraceuticals” refers to the link between the nutritional and pharmaceutical domains. Also, lately, many studies have been done to investigate the role of microbiota in maintaining health. There is the hypothesis that some of the health benefits of nutraceuticals are due to their ability to change the microbiota. The aim of this review was to emphasize the link between the most commonly used nutraceuticals, the microbiota and the health benefits. Methods We selected the articles in PubMed, published up to July 2017, that provided information about most used nutraceuticals, microbiota and health benefits. In this review, we incorporate evidence from various types of studies, including observational, in vitro and in vivo, clinical studies or animal experiments. Results The results demonstrate that many nutraceuticals change the composition of microbiota and can interfere with health status of the patients. Discussion There is evidence which sustains the importance of nutraceuticals in people’s health through microbiota but further studies are needed to complete the assessment of nutraceuticals in health benefit as a consequence of microbiota’s changing.
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Affiliation(s)
- Adrian Catinean
- Department of Internal Medicine/Faculty of Medicine, University of Medicine and Pharmacy of Cluj-Napoca, Cluj-Napoca, Romania
| | - Maria Adriana Neag
- Department of Pharmacology, Toxicology and Clinical Pharmacology/Faculty of Medicine, University of Medicine and Pharmacy of Cluj-Napoca, Cluj-Napoca, Romania
| | - Dana Maria Muntean
- Department of Pharmaceutical Technology and Biopharmaceutics/Faculty of Pharmacy, University of Medicine and Pharmacy of Cluj-Napoca, Cluj-Napoca, Romania
| | - Ioana Corina Bocsan
- Department of Pharmacology, Toxicology and Clinical Pharmacology/Faculty of Medicine, University of Medicine and Pharmacy of Cluj-Napoca, Cluj-Napoca, Romania
| | - Anca Dana Buzoianu
- Department of Pharmacology, Toxicology and Clinical Pharmacology/Faculty of Medicine, University of Medicine and Pharmacy of Cluj-Napoca, Cluj-Napoca, Romania
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22
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Evolutionary dynamics in the fungal polarization network, a mechanistic perspective. Biophys Rev 2017; 9:375-387. [PMID: 28812259 PMCID: PMC5578929 DOI: 10.1007/s12551-017-0286-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
Polarity establishment underlies proper cell cycle completion across virtually all organisms. Much progress has been made in generating an understanding of the structural and functional components of this process, especially in model species. Here we focus on the evolutionary dynamics of the fungal polarization protein network in order to determine general components and mechanistic principles, species- or lineage-specific adaptations and the evolvability of the network. The currently available genomic and proteomic screens in a variety of fungal species have shown three main characteristics: (1) certain proteins, processes and functions are conserved throughout the fungal clade; (2) orthologous functions can never be assumed, as various cases have been observed of homologous loci with dissimilar functions; (3) species have, typically, various species- or lineage-specific proteins incorporated in their polarization network. Further large-scale comparative and experimental studies, including those on non-model species representing the great fungal diversity, are needed to gain a better understanding of the evolutionary dynamics and generalities of the polarization network in fungi.
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23
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Zimmerman SP, Asokan SB, Kuhlman B, Bear JE. Cells lay their own tracks - optogenetic Cdc42 activation stimulates fibronectin deposition supporting directed migration. J Cell Sci 2017; 130:2971-2983. [PMID: 28754687 DOI: 10.1242/jcs.205948] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 12/30/2022] Open
Abstract
Rho GTPase family members are known regulators of directed migration and therefore play key roles in processes including development, the immune response and cancer metastasis. However, their individual contributions to these processes are complex. Here, we modify the activity of the two Rho GTPase family members Rac and Cdc42 by optogenetically recruiting specific guanine nucleotide exchange factor (GEF) DH or PH domains to defined regions of the cell membrane. We find that the localized activation of both GTPases produces lamellipodia in cells plated on a fibronectin substrate. By using a novel optotaxis assay, we show that biased activation can drive directional migration. Interestingly, in the absence of exogenous fibronectin, Rac activation is insufficient to produce stable lamellipodia or directional migration whereas Cdc42 activation is sufficient for these processes. We find that a remarkably small amount of fibronectin (<10 puncta per protrusion) is necessary to support stable GTPase-driven lamellipodia formation. Cdc42 bypasses the need for exogenous fibronectin by stimulating cellular fibronectin deposition under the newly formed lamellipodia.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Seth P Zimmerman
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sreeja B Asokan
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian Kuhlman
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James E Bear
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA .,Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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24
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Steury MD, McCabe LR, Parameswaran N. G Protein-Coupled Receptor Kinases in the Inflammatory Response and Signaling. Adv Immunol 2017; 136:227-277. [PMID: 28950947 DOI: 10.1016/bs.ai.2017.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
G protein-coupled receptor kinases (GRKs) are serine/threonine kinases that regulate a large and diverse class of G protein-coupled receptors (GPCRs). Through GRK phosphorylation and β-arrestin recruitment, GPCRs are desensitized and their signal terminated. Recent work on these kinases has expanded their role from canonical GPCR regulation to include noncanonical regulation of non-GPCR and nonreceptor substrates through phosphorylation as well as via scaffolding functions. Owing to these and other regulatory roles, GRKs have been shown to play a critical role in the outcome of a variety of physiological and pathophysiological processes including chemotaxis, signaling, migration, inflammatory gene expression, etc. This diverse set of functions for these proteins makes them popular targets for therapeutics. Role for these kinases in inflammation and inflammatory disease is an evolving area of research currently pursued in many laboratories. In this review, we describe the current state of knowledge on various GRKs pertaining to their role in inflammation and inflammatory diseases.
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Affiliation(s)
| | - Laura R McCabe
- Michigan State University, East Lansing, MI, United States
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25
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Bourgeois YXC, Delahaie B, Gautier M, Lhuillier E, Malé PJG, Bertrand JAM, Cornuault J, Wakamatsu K, Bouchez O, Mould C, Bruxaux J, Holota H, Milá B, Thébaud C. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160805. [PMID: 28386436 PMCID: PMC5367300 DOI: 10.1098/rsos.160805] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/12/2017] [Indexed: 06/07/2023]
Abstract
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a 'brown' ancestral population, the dominant 'grey' allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.
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Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Mathieu Gautier
- INRA, UMR 1062 CBGP (INRA, IRD, Cirad, Montpellier SupAgro), Campus de Baillarguet, 34988 Montferrier-sur-Lez, France
| | - Emeline Lhuillier
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- INRA, UAR1209, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Pierre-Jean G. Malé
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake Aichi 470-1192, Japan
| | - Olivier Bouchez
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Claire Mould
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Jade Bruxaux
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
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26
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Aslan E, Küçükoğlu N, Arslanyolu M. A comparative in-silico analysis of autophagy proteins in ciliates. PeerJ 2017; 5:e2878. [PMID: 28123910 PMCID: PMC5244887 DOI: 10.7717/peerj.2878] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 12/07/2016] [Indexed: 01/05/2023] Open
Abstract
Autophagy serves as a turnover mechanism for the recycling of redundant and/or damaged macromolecules present in eukaryotic cells to re-use them under starvation conditions via a double-membrane structure known as autophagosome. A set of eukaryotic genes called autophagy-related genes (ATGs) orchestrate this highly elaborative process. The existence of these genes and the role they play in different eukaryotes are well-characterized. However, little is known of their role in some eukaryotes such as ciliates. Here, we report the computational analyses of ATG genes in five ciliate genomes to understand their diversity. Our results show that Oxytricha trifallax is the sole ciliate which has a conserved Atg12 conjugation system (Atg5-Atg12-Atg16). Interestingly, Oxytricha Atg16 protein includes WD repeats in addition to its N-terminal Atg16 domain as is the case in multicellular organisms. Additionally, phylogenetic analyses revealed that E2-like conjugating protein Atg10 is only present in Tetrahymena thermophila. We fail to find critical autophagy components Atg5, Atg7 and Atg8 in the parasitic ciliate Ichthyophthirius multifiliis. Contrary to previous reports, we also find that ciliate genomes do not encode typical Atg1 since all the candidate sequences lack an Atg1-specific C-terminal domain which is essential for Atg1 complex formation. Consistent with the absence of Atg1, ciliates also lack other members of the Atg1 complex. However, the presence of Atg6 in all ciliates examined here may rise the possibility that autophagosome formation could be operated through Atg6 in ciliates, since Atg6 has been shown as an alternative autophagy inducer. In conclusion, our results highlight that Atg proteins are partially conserved in ciliates. This may provide a better understanding for the autophagic destruction of the parental macronucleus, a developmental process also known as programmed nuclear death in ciliates.
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Affiliation(s)
- Erhan Aslan
- Graduate School of Science, Department of Molecular Biology, Anadolu University, Eskişehir, Turkey
- Laboratory of Molecular Biotechnology and Enzymology, Faculty of Science, Department of Biology, Anadolu University, Eskişehir, Turkey
| | - Nurçin Küçükoğlu
- Graduate School of Science, Department of Molecular Biology, Anadolu University, Eskişehir, Turkey
- Laboratory of Molecular Biotechnology and Enzymology, Faculty of Science, Department of Biology, Anadolu University, Eskişehir, Turkey
| | - Muhittin Arslanyolu
- Laboratory of Molecular Biotechnology and Enzymology, Faculty of Science, Department of Biology, Anadolu University, Eskişehir, Turkey
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27
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Villa-Hernández S, Bueno A, Bermejo R. The Multiple Roles of Ubiquitylation in Regulating Challenged DNA Replication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:395-419. [PMID: 29357068 DOI: 10.1007/978-981-10-6955-0_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA replication is essential for the propagation of life and the development of complex organisms. However, replication is a risky process as it can lead to mutations and chromosomal alterations. Conditions challenging DNA synthesis by replicative polymerases or DNA helix unwinding, generally termed as replication stress, can halt replication fork progression. Stalled replication forks are unstable, and mechanisms exist to protect their integrity, which promote an efficient restart of DNA synthesis and counteract fork collapse characterized by the accumulation of DNA lesions and mutagenic events. DNA replication is a highly regulated process, and several mechanisms control replication timing and integrity both during unperturbed cell cycles and in response to replication stress. Work over the last two decades has revealed that key steps of DNA replication are controlled by conjugation of the small peptide ubiquitin. While ubiquitylation was traditionally linked to protein degradation, the complexity and flexibility of the ubiquitin system in regulating protein function have recently emerged. Here we review the multiple roles exerted by ubiquitin-conjugating enzymes and ubiquitin-specific proteases, as well as readers of ubiquitin chains, in the control of eukaryotic DNA replication and replication-coupled DNA damage tolerance and repair.
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Affiliation(s)
| | - Avelino Bueno
- Instituto de Biología Molecular y Celular del Cáncer (USAL/CSIC), Salamanca, Spain.,Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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28
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Simões J, Bezerra AR, Moura GR, Araújo H, Gut I, Bayes M, Santos MAS. The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons. Front Microbiol 2016; 7:401. [PMID: 27065968 PMCID: PMC4814463 DOI: 10.3389/fmicb.2016.00401] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/14/2016] [Indexed: 12/31/2022] Open
Abstract
The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients, and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions, CUG sites incorporate leucine (3% of the times) and serine (97% of the times) on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT) strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.
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Affiliation(s)
- João Simões
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Ana R Bezerra
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Gabriela R Moura
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Hugo Araújo
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Ivo Gut
- Centro Nacional de Análises Genómico, Parc Científic Barcelona, Spain
| | - Mónica Bayes
- Centro Nacional de Análises Genómico, Parc Científic Barcelona, Spain
| | - Manuel A S Santos
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
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29
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Sarnelli G, Gigli S, Capoccia E, Iuvone T, Cirillo C, Seguella L, Nobile N, D'Alessandro A, Pesce M, Steardo L, Cuomo R, Esposito G. Palmitoylethanolamide Exerts Antiproliferative Effect and Downregulates VEGF Signaling in Caco-2 Human Colon Carcinoma Cell Line Through a Selective PPAR-α-Dependent Inhibition of Akt/mTOR Pathway. Phytother Res 2016; 30:963-70. [PMID: 26929026 DOI: 10.1002/ptr.5601] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 01/17/2023]
Abstract
Palmitoylethanolamide (PEA) is a nutraceutical compound that has been demonstrated to improve intestinal inflammation. We aimed at evaluating its antiproliferative and antiangiogenic effects in human colon adenocarcinoma Caco-2 cell line. Caco-2 cells were treated with increasing concentrations of PEA (0.001, 0.01 and 0.1 μM) in the presence of peroxisome proliferator-activated receptor-a (PPAR-α) or PPAR-γ antagonists. Cell proliferation was evaluated by performing a MTT assay. Vascular endothelial growth factor (VEGF) release was estimated by ELISA, while the expression of VEGF receptor and the activation of the Akt/mammalian target of rapamycin (mTOR) pathway were evaluated by western blot analysis. PEA caused a significant and concentration-dependent decrease of Caco-2 cell proliferation at 48 h. PEA administration significantly reduced in a concentration-dependent manner VEGF secretion and VEGF receptor expression. Inhibition of Akt phosphorylation and a downstream decrease of phospho-mTOR and of p-p70S6K were observed as compared with untreated cells. PPAR-α, but not PPAR-γ antagonist, reverted all effects of PEA. PEA is able to decrease cell proliferation and angiogenesis. The antiangiogenic effect of PEA depends on the specific inhibition of the AkT/mTOR axis, through the activation of PPAR-α pathway. If supported by in vivo models, our data pave the way to PEA co-administration to the current chemotherapeutic regimens for colon carcinoma. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Giovanni Sarnelli
- Department of Clinical Medicine and Surgery, 'Federico II' University of Naples, Naples, Italy
| | - Stefano Gigli
- Department of Physiology and Pharmacology 'Vittorio Erspamer', La Sapienza University of Rome, Rome, Italy
| | - Elena Capoccia
- Department of Physiology and Pharmacology 'Vittorio Erspamer', La Sapienza University of Rome, Rome, Italy
| | - Teresa Iuvone
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Carla Cirillo
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven, Belgium
| | - Luisa Seguella
- Department of Physiology and Pharmacology 'Vittorio Erspamer', La Sapienza University of Rome, Rome, Italy
| | - Nicola Nobile
- Department of Physiology and Pharmacology 'Vittorio Erspamer', La Sapienza University of Rome, Rome, Italy
| | - Alessandra D'Alessandro
- Department of Clinical Medicine and Surgery, 'Federico II' University of Naples, Naples, Italy
| | - Marcella Pesce
- Department of Clinical Medicine and Surgery, 'Federico II' University of Naples, Naples, Italy
| | - Luca Steardo
- Department of Physiology and Pharmacology 'Vittorio Erspamer', La Sapienza University of Rome, Rome, Italy
| | - Rosario Cuomo
- Department of Clinical Medicine and Surgery, 'Federico II' University of Naples, Naples, Italy
| | - Giuseppe Esposito
- Department of Physiology and Pharmacology 'Vittorio Erspamer', La Sapienza University of Rome, Rome, Italy
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30
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Bernadotte A, Mikhelson VM, Spivak IM. Markers of cellular senescence. Telomere shortening as a marker of cellular senescence. Aging (Albany NY) 2016; 8:3-11. [PMID: 26805432 PMCID: PMC4761709 DOI: 10.18632/aging.100871] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The cellular senescence definition comes to the fact of cells irreversible proliferation disability. Besides the cell cycle arrest, senescent cells go through some morphological, biochemical, and functional changes which are the signs of cellular senescence. The senescent cells (including replicative senescence and stress-induced premature senescence) of all the tissues look alike. They are metabolically active and possess the set of characteristics in vitro and in vivo, which are known as biomarkers of aging and cellular senescence. Among biomarkers of cellular senescence telomere shortening is a rather elegant frequently used biomarker. Validity of telomere shortening as a marker for cellular senescence is based on theoretical and experimental data.
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Affiliation(s)
- Alexandra Bernadotte
- Karolinska Institute, Department of Medical Biochemistry and Biophysics, Stockholm, 14157, Sweden
- St. Petersburg Institute of Bioregulation and Gerontology, Russian Academy of Sciences, Saint-Petersburg, 197110 Russia
| | - Victor M. Mikhelson
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, 194064, Russia
| | - Irina M. Spivak
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, 194064, Russia
- Saint-Petersburg's State University, Saint-Petersburg, 199034, Russia
- Saint-Petersburg's Polytechnic State University, Saint-Petersburg, 195251 Russia
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31
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Liu X, Wang X, Yang X, Liu S, Jiang L, Qu Y, Hu L, Ouyang Q, Tang C. Reliable cell cycle commitment in budding yeast is ensured by signal integration. eLife 2015; 4. [PMID: 25590650 PMCID: PMC4378612 DOI: 10.7554/elife.03977] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 01/07/2015] [Indexed: 12/29/2022] Open
Abstract
Cell fate decisions are critical for life, yet little is known about how their
reliability is achieved when signals are noisy and fluctuating with time. In this
study, we show that in budding yeast, the decision of cell cycle commitment (Start)
is determined by the time integration of its triggering signal Cln3. We further
identify the Start repressor, Whi5, as the integrator. The instantaneous kinase
activity of Cln3-Cdk1 is recorded over time on the phosphorylated Whi5, and the
decision is made only when phosphorylated Whi5 reaches a threshold. Cells adjust the
threshold by modulating Whi5 concentration in different nutrient conditions to
coordinate growth and division. Our work shows that the strategy of signal
integration, which was previously found in decision-making behaviors of animals, is
adopted at the cellular level to reduce noise and minimize uncertainty. DOI:http://dx.doi.org/10.7554/eLife.03977.001 Budding yeast and other single-celled organisms can reproduce by dividing to produce
two daughter cells. The timing of the cell division is critical because if the cell
is still small when it divides, the resulting daughter cells may not be big enough to
survive. In budding yeast, the irreversible decision to divide—known as the
‘Start’ checkpoint—is only made once a cell reaches a certain
size and is triggered by a protein called Cln3. This protein controls the activity of
another protein called Whi5, which normally prevents the cell from dividing by
switching off particular genes. Cln3 adds phosphate groups to Whi5 to make
‘phosphorylated Whi5’, which allows the genes involved in cell division
to be switched on. It is commonly believed that the level of Cln3 reflects the size of the cell and the
nutrient conditions. Therefore, one model of cell division proposes that the cell
passes the Start checkpoint when the level of Cln3 reaches a threshold value.
However, levels of the Cln3 protein in cells can naturally fluctuate, and computer
simulations based on this model showed that this would not produce reliable decisions
on when to divide. So how do cells manage to distinguish noise from the genuine
signals that indicate it is the right time to divide? To address this question, Liu et al. studied yeast cells containing an artificial
version of the gene encoding the Cln3 protein whose levels could be adjusted by
adding a particular chemical. This revealed that cells with higher levels of Cln3
passed through the Start checkpoint sooner than cells that had lower levels of
Cln3. The observation suggests that cells add up the amount of Cln3 present over a period
of time to see if this reaches the threshold needed for the Start checkpoint. This
could be possible if, instead of sensing Cln3 levels directly, the cell senses the
accumulation of phosphorylated Whi5. To test this idea, Liu et al. carried out
additional experiments and found that the decision to pass the Start checkpoint only
occurs when the amount of phosphorylated Whi5 reaches a certain threshold. The cells are able to coordinate their growth and division under different nutrient
conditions by altering the threshold of phosphorylated Whi5. When the nutrient supply
is poor, more phosphorylated Whi5 needs to be accumulated to allow the cell to pass
the Start checkpoint. In this way, cells adjust when they divide according to
nutrient conditions. Similar strategies may be found in other signaling or
decision-making systems. DOI:http://dx.doi.org/10.7554/eLife.03977.002
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Affiliation(s)
- Xili Liu
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Xin Wang
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Xiaojing Yang
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Sen Liu
- Institute of Molecular Biology, College of Medical Science, China Three Gorges University, Yichang, China
| | - Lingli Jiang
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Yimiao Qu
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Lufeng Hu
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Qi Ouyang
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing, China
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32
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Tamura N, Draviam VM. Microtubule plus-ends within a mitotic cell are 'moving platforms' with anchoring, signalling and force-coupling roles. Open Biol 2012; 2:120132. [PMID: 23226599 PMCID: PMC3513837 DOI: 10.1098/rsob.120132] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/01/2012] [Indexed: 12/21/2022] Open
Abstract
The microtubule polymer grows and shrinks predominantly from one of its ends called the 'plus-end'. Plus-end regulation during interphase is well understood. However, mitotic regulation of plus-ends is only beginning to be understood in mammalian cells. During mitosis, the plus-ends are tethered to specialized microtubule capture sites. At these sites, plus-end-binding proteins are loaded and unloaded in a regulated fashion. Proper tethering of plus-ends to specialized sites is important so that the microtubule is able to translate its growth and shrinkage into pushing and pulling forces that move bulky subcellular structures. We discuss recent advances on how mitotic plus-ends are tethered to distinct subcellular sites and how plus-end-bound proteins can modulate the forces that move subcellular structures. Using end binding 1 (EB1) as a prototype plus-end-binding protein, we highlight the complex network of plus-end-binding proteins and their regulation through phosphorylation. Finally, we develop a speculative 'moving platform' model that illustrates the plus-end's role in distinguishing correct versus incorrect microtubule interactions.
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Affiliation(s)
| | - Viji M. Draviam
- Department of Genetics, University of Cambridge, Downing Site, Downing Street, Cambridge CB2 3EH, UK
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