The Septin Cytoskeleton in Heart Development and Disease
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A Complete Compendium of Crystal Structures for the Human SEPT3 Subgroup Reveals Functional Plasticity at a Specific Septin Inte
research papers A complete compendium of crystal structures for IUCrJ the human SEPT3 subgroup reveals functional ISSN 2052-2525 plasticity at a specific septin interface BIOLOGYjMEDICINE Danielle Karoline Silva do Vale Castro,a,b‡ Sabrina Matos de Oliveira da Silva,a,b‡ Humberto D’Muniz Pereira,a Joci Neuby Alves Macedo,a,c Diego Antonio Leonardo,a Napolea˜o Fonseca Valadares,d Patricia Suemy Kumagai,a Jose´ Branda˜o- Received 2 December 2019 Neto,e Ana Paula Ulian Arau´joa and Richard Charles Garratta* Accepted 3 March 2020 aInstituto de Fı´sica de Sa˜o Carlos, Universidade de Sa˜o Paulo, Avenida Joao Dagnone 1100, Sa˜o Carlos-SP 13563-723, b Edited by Z.-J. Liu, Chinese Academy of Brazil, Instituto de Quı´mica de Sa˜o Carlos, Universidade de Sa˜o Paulo, Avenida Trabalhador Sa˜o-carlense 400, c Sciences, China Sa˜o Carlos-SP 13566-590, Brazil, Federal Institute of Education, Science and Technology of Rondonia, Rodovia BR-174, Km 3, Vilhena-RO 76980-000, Brazil, dDepartamento de Biologia Celular, Universidade de Brası´lia, Instituto de Cieˆncias Biolo´gicas, Brası´lia-DF 70910900, Brazil, and eDiamond Light Source, Diamond House, Harwell Science and Innovation ‡ These authors contributed equally to this Campus, Didcot OX11 0DE, United Kingdom. *Correspondence e-mail: [email protected] work. Keywords: septins; GTP binding/hydrolysis; Human septins 3, 9 and 12 are the only members of a specific subgroup of septins filaments; protein structure; X-ray that display several unusual features, including the absence of a C-terminal crystallography. coiled coil. This particular subgroup (the SEPT3 septins) are present in rod-like octameric protofilaments but are lacking in similar hexameric assemblies, which PDB references: SEPT3G–GTP S, 4z51; only contain representatives of the three remaining subgroups. -
Dissection of Molecular Assembly Dynamics by Tracking Orientation
Dissection of molecular assembly dynamics by tracking PNAS PLUS orientation and position of single molecules in live cells Shalin B. Mehtaa,1, Molly McQuilkenb,c, Patrick J. La Riviered, Patricia Occhipintib,c, Amitabh Vermaa, Rudolf Oldenbourga,e, Amy S. Gladfeltera,b,c, and Tomomi Tania,2 aEugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543; bDepartment of Biological Sciences, Dartmouth College, Hanover, NH 03755; cDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; dDepartment of Radiology, University of Chicago, Chicago, IL 60637; and ePhysics Department, Brown University, Providence, RI 02912 Edited by Jennifer Lippincott-Schwartz, National Institutes of Health, Bethesda, MD, and approved August 19, 2016 (received for review May 12, 2016) Regulation of order, such as orientation and conformation, drives excitation (3–5, 14–18) or polarization-resolved detection (1, 2, 19– the function of most molecular assemblies in living cells but 21) has allowed measurement of orientations of fluorophores. remains difficult to measure accurately through space and time. For fluorescent assemblies that exhibit simple geometries, such We built an instantaneous fluorescence polarization microscope, as planar (3), spherical (2), or cylindrical (19) shapes, two or- which simultaneously images position and orientation of fluorophores thogonal polarization-resolved measurements suffice to retrieve in living cells with single-molecule sensitivity and a time resolution fluorophore orientations relative to these geometries. However, of 100 ms. We developed image acquisition and analysis methods unbiased measurement of dipole orientation in a complex as- to track single particles that interact with higher-order assemblies sembly requires exciting or analyzing the fluorescent dipoles using of molecules. -
Supplementary Information Integrative Analyses of Splicing in the Aging Brain: Role in Susceptibility to Alzheimer’S Disease
Supplementary Information Integrative analyses of splicing in the aging brain: role in susceptibility to Alzheimer’s Disease Contents 1. Supplementary Notes 1.1. Religious Orders Study and Memory and Aging Project 1.2. Mount Sinai Brain Bank Alzheimer’s Disease 1.3. CommonMind Consortium 1.4. Data Availability 2. Supplementary Tables 3. Supplementary Figures Note: Supplementary Tables are provided as separate Excel files. 1. Supplementary Notes 1.1. Religious Orders Study and Memory and Aging Project Gene expression data1. Gene expression data were generated using RNA- sequencing from Dorsolateral Prefrontal Cortex (DLPFC) of 540 individuals, at an average sequence depth of 90M reads. Detailed description of data generation and processing was previously described2 (Mostafavi, Gaiteri et al., under review). Samples were submitted to the Broad Institute’s Genomics Platform for transcriptome analysis following the dUTP protocol with Poly(A) selection developed by Levin and colleagues3. All samples were chosen to pass two initial quality filters: RNA integrity (RIN) score >5 and quantity threshold of 5 ug (and were selected from a larger set of 724 samples). Sequencing was performed on the Illumina HiSeq with 101bp paired-end reads and achieved coverage of 150M reads of the first 12 samples. These 12 samples will serve as a deep coverage reference and included 2 males and 2 females of nonimpaired, mild cognitive impaired, and Alzheimer's cases. The remaining samples were sequenced with target coverage of 50M reads; the mean coverage for the samples passing QC is 95 million reads (median 90 million reads). The libraries were constructed and pooled according to the RIN scores such that similar RIN scores would be pooled together. -
Diminished Dosage of 22Q11 Genes Disrupts Neurogenesis and Cortical Development in a Mouse Model of 22Q11 Deletion/Digeorge Syndrome
Diminished dosage of 22q11 genes disrupts neurogenesis and cortical development in a mouse model of 22q11 deletion/DiGeorge syndrome Daniel W. Meechana, Eric S. Tuckera, Thomas M. Maynarda, and Anthony-Samuel LaMantiaa,b,1 aDepartment of Cell and Molecular Physiology and bNeuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599 Edited by Pasko Rakic, Yale University School of Medicine, New Haven, CT, and approved July 22, 2009 (received for review May 28, 2009) The 22q11 deletion (or DiGeorge) syndrome (22q11DS), the result of flect changes in cortical neurogenesis. We focused on two a 1.5- to 3-megabase hemizygous deletion on human chromosome 22, distinct classes of cortical progenitors: basal progenitors–transit results in dramatically increased susceptibility for ‘‘diseases of cortical amplifying progenitors in the cortical subventricular zone connectivity’’ thought to arise during development, including schizo- (SVZ)–and apical progenitors–self-renewing radial glial stem phrenia and autism. We show that diminished dosage of the genes cells present in the cortical VZ. Each class can be recognized deleted in the 1.5-megabase 22q11 minimal critical deleted region in with combinations of proliferative and molecular markers (Fig. a mouse model of 22q11DS specifically compromises neurogenesis 1). We found reduced frequency of mitotic basal progenitors, and subsequent differentiation in the cerebral cortex. Proliferation of identified by phosphohistone 3 labeling (PH3; a G2/M-phase basal, but not apical, progenitors is disrupted, and subsequently, the cell-cycle marker) as well as SVZ location, throughout the frequency of layer 2/3, but not layer 5/6, projection neurons is altered. -
Protein Kinase A-Mediated Septin7 Phosphorylation Disrupts Septin Filaments and Ciliogenesis
cells Article Protein Kinase A-Mediated Septin7 Phosphorylation Disrupts Septin Filaments and Ciliogenesis Han-Yu Wang 1,2, Chun-Hsiang Lin 1, Yi-Ru Shen 1, Ting-Yu Chen 2,3, Chia-Yih Wang 2,3,* and Pao-Lin Kuo 1,2,4,* 1 Department of Obstetrics and Gynecology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; [email protected] (H.-Y.W.); [email protected] (C.-H.L.); [email protected] (Y.-R.S.) 2 Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; [email protected] 3 Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan 4 Department of Obstetrics and Gynecology, National Cheng-Kung University Hospital, Tainan 704, Taiwan * Correspondence: [email protected] (C.-Y.W.); [email protected] (P.-L.K.); Tel.: +886-6-2353535 (ext. 5338); (C.-Y.W.)+886-6-2353535 (ext. 5262) (P.-L.K.) Abstract: Septins are GTP-binding proteins that form heteromeric filaments for proper cell growth and migration. Among the septins, septin7 (SEPT7) is an important component of all septin filaments. Here we show that protein kinase A (PKA) phosphorylates SEPT7 at Thr197, thus disrupting septin filament dynamics and ciliogenesis. The Thr197 residue of SEPT7, a PKA phosphorylating site, was conserved among different species. Treatment with cAMP or overexpression of PKA catalytic subunit (PKACA2) induced SEPT7 phosphorylation, followed by disruption of septin filament formation. Constitutive phosphorylation of SEPT7 at Thr197 reduced SEPT7-SEPT7 interaction, but did not affect SEPT7-SEPT6-SEPT2 or SEPT4 interaction. -
1 Supporting Information for a Microrna Network Regulates
Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia. -
Why Cells and Viruses Cannot Survive Without an ESCRT
cells Review Why Cells and Viruses Cannot Survive without an ESCRT Arianna Calistri * , Alberto Reale, Giorgio Palù and Cristina Parolin Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; [email protected] (A.R.); [email protected] (G.P.); [email protected] (C.P.) * Correspondence: [email protected] Abstract: Intracellular organelles enwrapped in membranes along with a complex network of vesicles trafficking in, out and inside the cellular environment are one of the main features of eukaryotic cells. Given their central role in cell life, compartmentalization and mechanisms allowing their maintenance despite continuous crosstalk among different organelles have been deeply investigated over the past years. Here, we review the multiple functions exerted by the endosomal sorting complex required for transport (ESCRT) machinery in driving membrane remodeling and fission, as well as in repairing physiological and pathological membrane damages. In this way, ESCRT machinery enables different fundamental cellular processes, such as cell cytokinesis, biogenesis of organelles and vesicles, maintenance of nuclear–cytoplasmic compartmentalization, endolysosomal activity. Furthermore, we discuss some examples of how viruses, as obligate intracellular parasites, have evolved to hijack the ESCRT machinery or part of it to execute/optimize their replication cycle/infection. A special emphasis is given to the herpes simplex virus type 1 (HSV-1) interaction with the ESCRT proteins, considering the peculiarities of this interplay and the need for HSV-1 to cross both the nuclear-cytoplasmic and the cytoplasmic-extracellular environment compartmentalization to egress from infected cells. Citation: Calistri, A.; Reale, A.; Palù, Keywords: ESCRT; viruses; cellular membranes; extracellular vesicles; HSV-1 G.; Parolin, C. -
Phylogenetic and Evolutionary Analysis of the Septin Protein Family in Metazoan
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 581 (2007) 5526–5532 Phylogenetic and evolutionary analysis of the septin protein family in metazoan Lihuan Cao1, Xiangming Ding1, Wenbo Yu, Xianmei Yang, Suqin Shen, Long Yu* State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, PR China Received 9 August 2007; revised 11 October 2007; accepted 19 October 2007 Available online 29 October 2007 Edited by Takashi Gojobori have a P-loop [8,9] which is defined by the Walker A motif Abstract Septins, a conserved family of cytoskeletal GTP- binding proteins, were presented in diverse eukaryotes. Here, a (GxxGxGKST), Walker B motif (DxxG), and the GTP-speci- comprehensive phylogenetic and evolutionary analysis for septin ficity motif (xKxD). Septins differ from most other members of proteins in metazoan was carried out. First, we demonstrated this subclass in that they lack an asparagine at position 1 of the that all septin proteins in metazoan could be clustered into four GTP-specificity motif (i.e. not NKxD, but AKAD or GKAD) subgroups, and the representative homologue of every subgroup [7]. Recently, the crystal structures of the human SEPT2 G was presented in the non-vertebrate chordate Ciona intestinalis, domain and the heterotrimeric human SEPT2-SEPT6-SEPT7 indicating that the emergence of the four septin subgroups should complex had been determined. The septin complex structure have occurred prior to divergence of vertebrates and inverte- revealed a universal bipolar polymer building block, composed brates, and the expansion of the septin gene number in verte- of an extended G domain, which forms oligomers and fila- brates was mainly by the duplication of pre-existing genes ments by conserved interactions between adjacent nucleotide- rather than by the appearance of new septin subgroup. -
Development and Applications of Superfolder and Split Fluorescent Protein Detection Systems in Biology
International Journal of Molecular Sciences Review Development and Applications of Superfolder and Split Fluorescent Protein Detection Systems in Biology Jean-Denis Pedelacq 1,* and Stéphanie Cabantous 2,* 1 Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France 2 Centre de Recherche en Cancérologie de Toulouse (CRCT), Inserm, Université Paul Sabatier-Toulouse III, CNRS, 31037 Toulouse, France * Correspondence: [email protected] (J.-D.P.); [email protected] (S.C.) Received: 15 June 2019; Accepted: 8 July 2019; Published: 15 July 2019 Abstract: Molecular engineering of the green fluorescent protein (GFP) into a robust and stable variant named Superfolder GFP (sfGFP) has revolutionized the field of biosensor development and the use of fluorescent markers in diverse area of biology. sfGFP-based self-associating bipartite split-FP systems have been widely exploited to monitor soluble expression in vitro, localization, and trafficking of proteins in cellulo. A more recent class of split-FP variants, named « tripartite » split-FP,that rely on the self-assembly of three GFP fragments, is particularly well suited for the detection of protein–protein interactions. In this review, we describe the different steps and evolutions that have led to the diversification of superfolder and split-FP reporter systems, and we report an update of their applications in various areas of biology, from structural biology to cell biology. Keywords: fluorescent protein; superfolder; split-GFP; bipartite; tripartite; folding; PPI 1. Superfolder Fluorescent Proteins: Progenitor of Split Fluorescent Protein (FP) Systems Previously described mutations that improve the physical properties and expression of green fluorescent protein (GFP) color variants in the host organism have already been the subject of several reviews [1–4] and will not be described here. -
Proteomic Profiling of the Oncogenic Septin 9 Reveals Isoform-Specific
bioRxiv preprint doi: https://doi.org/10.1101/566513; this version posted March 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Proteomic profiling of the oncogenic septin 9 reveals isoform-specific interactions in breast cancer cells Louis Devlina,b, George Perkinsb, Jonathan R. Bowena, Cristina Montagnac and Elias T. Spiliotisa* aDepartment of Biology, Drexel University, Philadelphia, PA 19095, USA bSanofi Pasteur, Swiftwater, PA 18370, USA cDepartments of Genetics and Pathology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA *Corresponding author: Elias T. Spiliotis, Department of Biology, Drexel University, PISB 423, 3245 Chestnut St, Philadelphia, PA 19104, USA E-mail: [email protected] Phone: 215-571-3552 Fax: 215-895-1273 Key words: septins, SEPT9 isoforms, breast cancer, septin interactome 1 bioRxiv preprint doi: https://doi.org/10.1101/566513; this version posted March 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Septins are a family of multimeric GTP-binding proteins, which are abnormally expressed in cancer. Septin 9 (SEPT9) is an essential and ubiquitously expressed septin with multiple isoforms, which have differential expression patterns and effects in breast cancer cells. It is unknown, however, if SEPT9 isoforms associate with different molecular networks and functions. Here, we performed a proteomic screen in MCF-7 breast cancer cells to identify the interactome of GFP-SEPT9 isoforms 1, 4 and 5, which vary significantly in their N-terminal extensions. -
A DNA Methylation Biomarker of Alcohol Consumption
OPEN Molecular Psychiatry (2018) 23, 422–433 www.nature.com/mp ORIGINAL ARTICLE A DNA methylation biomarker of alcohol consumption C Liu1,2,3,55, RE Marioni4,5,6,55, ÅK Hedman7,55, L Pfeiffer8,9,55, P-C Tsai10,55, LM Reynolds11,55, AC Just12,55, Q Duan13,55, CG Boer14,55, T Tanaka15,55, CE Elks16, S Aslibekyan17, JA Brody18, B Kühnel8,9, C Herder19,20, LM Almli21, D Zhi22, Y Wang23, T Huan1,2,CYao1,2, MM Mendelson1,2, R Joehanes1,2,24, L Liang25, S-A Love23, W Guan26, S Shah6,27, AF McRae6,27, A Kretschmer8,9, H Prokisch28,29, K Strauch30,31, A Peters8,9,32, PM Visscher4,6,27,NRWray6,27, X Guo33, KL Wiggins18, AK Smith21, EB Binder34, KJ Ressler35, MR Irvin17, DM Absher36, D Hernandez37, L Ferrucci15, S Bandinelli38, K Lohman11, J Ding39, L Trevisi40, S Gustafsson7, JH Sandling41,42, L Stolk14, AG Uitterlinden14,43,IYet10, JE Castillo-Fernandez10, TD Spector10, JD Schwartz44, P Vokonas45, L Lind46,YLi47, M Fornage48, DK Arnett49, NJ Wareham16, N Sotoodehnia18, KK Ong16, JBJ van Meurs14, KN Conneely50, AA Baccarelli51, IJ Deary4,52, JT Bell10, KE North23,56, Y Liu11,56, M Waldenberger8,9,56, SJ London53,56, E Ingelsson7,54,56 and D Levy1,2,56 The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (ntotal = 13 317; 54% women; mean age across cohorts 42–76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples. -
Actin, Microtubule, Septin and ESCRT Filament Remodeling During Late Steps of Cytokinesis Cyril Addi, Jian Bai, Arnaud Echard
Actin, microtubule, septin and ESCRT filament remodeling during late steps of cytokinesis Cyril Addi, Jian Bai, Arnaud Echard To cite this version: Cyril Addi, Jian Bai, Arnaud Echard. Actin, microtubule, septin and ESCRT filament remodel- ing during late steps of cytokinesis. Current Opinion in Cell Biology, Elsevier, 2018, 50, pp.27-34. 10.1016/j.ceb.2018.01.007. hal-02114062 HAL Id: hal-02114062 https://hal.archives-ouvertes.fr/hal-02114062 Submitted on 29 Apr 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License Actin, microtubule, septin and ESCRT filament remodeling during late steps of cytokinesis Cyril Addi1,2,3,#, Jian Bai1,2,3,# and Arnaud Echard1,2 1 Membrane Traffic and Cell Division Lab, Cell Biology and Infection department Institut Pasteur, 25–28 rue du Dr Roux, 75724 Paris cedex 15, France 2 Centre National de la Recherche Scientifique CNRS UMR3691, 75015 Paris, France 3 Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, Institut de formation doctorale, 75252 Paris, France # equal contribution, alphabetical order correspondence: [email protected] 1 ABSTRACT Cytokinesis is the process by which a mother cell is physically cleaved into two daughter cells.