Microtubule-Based Transport and the Distribution, Tethering, and Organization of Organelles
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Mechanical Design of Translocating Motor Proteins
Cell Biochem Biophys (2009) 54:11–22 DOI 10.1007/s12013-009-9049-4 REVIEW PAPER Mechanical Design of Translocating Motor Proteins Wonmuk Hwang Æ Matthew J. Lang Published online: 19 May 2009 Ó Humana Press Inc. 2009 Abstract Translocating motors generate force and move Introduction along a biofilament track to achieve diverse functions including gene transcription, translation, intracellular cargo Motor proteins form distinct classes in the protein universe transport, protein degradation, and muscle contraction. as they can convert chemical energy directly into mechan- Advances in single molecule manipulation experiments, ical work. Among them, translocating motors move along structural biology, and computational analysis are making biopolymer tracks, such as nucleic acids, polypeptides, or it possible to consider common mechanical design princi- quaternary biofilament structures like F-actin or microtu- ples of these diverse families of motors. Here, we propose a bule (Kolomeisky and Fisher proposed the term ‘‘translo- mechanical parts list that include track, energy conversion case’’ for these motors [41]. However, we prefer to use machinery, and moving parts. Energy is supplied not just ‘‘translocating motor,’’ since translocase refers to mem- by burning of a fuel molecule, but there are other sources brane-bound motors such as SecA, whose function is to or sinks of free energy, by binding and release of a fuel or translocate a protein across the membrane [24]). Movement products, or similarly between the motor and the track. is an essential part of their function. For example, RNA Dynamic conformational changes of the motor domain can polymerase (RNAP) walks along the DNA molecule and be regarded as controlling the flow of free energy to and transcribes the genetic code into RNA [25]. -
Regulation of Cardiovascular Homeostasis by Autophagy
Georgia State University ScholarWorks @ Georgia State University Chemistry Dissertations Department of Chemistry 12-16-2020 Regulation Of Cardiovascular Homeostasis By Autophagy Jing Mu Georgia State University Follow this and additional works at: https://scholarworks.gsu.edu/chemistry_diss Recommended Citation Mu, Jing, "Regulation Of Cardiovascular Homeostasis By Autophagy." Dissertation, Georgia State University, 2020. https://scholarworks.gsu.edu/chemistry_diss/190 This Dissertation is brought to you for free and open access by the Department of Chemistry at ScholarWorks @ Georgia State University. It has been accepted for inclusion in Chemistry Dissertations by an authorized administrator of ScholarWorks @ Georgia State University. For more information, please contact [email protected]. REGULATION OF CARDIOVASCULAR HOMEOSTASIS BY AUTOPHAGY by JING MU Under the Direction of Ming-hui Zou, MD/PhD ABSTRACT Macroautophagy (hereafter autophagy) is a fundamental cellular process that removes unnecessary or dysfunctional components. It allows the orderly degradation and recycling of cellular components. Mitophagy refers to the selective removal of damaged mitochondria via autophagy pathway. In addition to utilizing core autophagic machinery components, mitophagy exploits a variety of molecules, such as PTEN-induced putative kinase protein 1 (PINK1) and Parkin, to identify and eliminate damaged or superfluous mitochondria. Dysregulation of autophagy and mitophagy contributes to a variety of human disorders, including cardiovascular diseases, such as atherosclerosis and diabetic cardiomyopathy. Vascular smooth muscle cells (VSMCs) are a major component of the vascular media, and are vital for maintaining vessel homeostasis. Migration of VSMCs from the media to intima occurs during the development of atherosclerosis. Although alterations in autophagy activity have been reported in atherosclerosis, further investigation is required to delineate the mechanism by which autophagy regulates microtubule stability and cell migration. -
Theory of Cytoskeletal Reorganization During Crosslinker-Mediated Mitotic Spindle Assembly
bioRxiv preprint doi: https://doi.org/10.1101/419135; this version posted March 1, 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. Theory of cytoskeletal reorganization during crosslinker-mediated mitotic spindle assembly A. R. Lamson, C. J. Edelmaier, M. A. Glaser, and M. D. Betterton Abstract Cells grow, move, and respond to outside stimuli by large-scale cytoskeletal reorganization. A prototypical example of cytoskeletal remodeling is mitotic spindle assembly, during which micro- tubules nucleate, undergo dynamic instability, bundle, and organize into a bipolar spindle. Key mech- anisms of this process include regulated filament polymerization, crosslinking, and motor-protein activity. Remarkably, using passive crosslinkers, fission yeast can assemble a bipolar spindle in the absence of motor proteins. We develop a torque-balance model that describes this reorganization due to dynamic microtubule bundles, spindle-pole bodies, the nuclear envelope, and passive crosslink- ers to predict spindle-assembly dynamics. We compare these results to those obtained with kinetic Monte Carlo-Brownian dynamics simulations, which include crosslinker-binding kinetics and other stochastic effects. Our results show that rapid crosslinker reorganization to microtubule overlaps facilitates crosslinker-driven spindle assembly, a testable prediction for future experiments. Combin- ing these two modeling techniques, we illustrate a general method for studying cytoskeletal network reorganization. 1 bioRxiv preprint doi: https://doi.org/10.1101/419135; this version posted March 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. -
Construction and Loss of Bacterial Flagellar Filaments
biomolecules Review Construction and Loss of Bacterial Flagellar Filaments Xiang-Yu Zhuang and Chien-Jung Lo * Department of Physics and Graduate Institute of Biophysics, National Central University, Taoyuan City 32001, Taiwan; [email protected] * Correspondence: [email protected] Received: 31 July 2020; Accepted: 4 November 2020; Published: 9 November 2020 Abstract: The bacterial flagellar filament is an extracellular tubular protein structure that acts as a propeller for bacterial swimming motility. It is connected to the membrane-anchored rotary bacterial flagellar motor through a short hook. The bacterial flagellar filament consists of approximately 20,000 flagellins and can be several micrometers long. In this article, we reviewed the experimental works and models of flagellar filament construction and the recent findings of flagellar filament ejection during the cell cycle. The length-dependent decay of flagellar filament growth data supports the injection-diffusion model. The decay of flagellar growth rate is due to reduced transportation of long-distance diffusion and jamming. However, the filament is not a permeant structure. Several bacterial species actively abandon their flagella under starvation. Flagellum is disassembled when the rod is broken, resulting in an ejection of the filament with a partial rod and hook. The inner membrane component is then diffused on the membrane before further breakdown. These new findings open a new field of bacterial macro-molecule assembly, disassembly, and signal transduction. Keywords: self-assembly; injection-diffusion model; flagellar ejection 1. Introduction Since Antonie van Leeuwenhoek observed animalcules by using his single-lens microscope in the 18th century, we have entered a new era of microbiology. -
Review of Molecular Motors
REVIEWS CYTOSKELETAL MOTORS Moving into the cell: single-molecule studies of molecular motors in complex environments Claudia Veigel*‡ and Christoph F. Schmidt§ Abstract | Much has been learned in the past decades about molecular force generation. Single-molecule techniques, such as atomic force microscopy, single-molecule fluorescence microscopy and optical tweezers, have been key in resolving the mechanisms behind the power strokes, ‘processive’ steps and forces of cytoskeletal motors. However, it remains unclear how single force generators are integrated into composite mechanical machines in cells to generate complex functions such as mitosis, locomotion, intracellular transport or mechanical sensory transduction. Using dynamic single-molecule techniques to track, manipulate and probe cytoskeletal motor proteins will be crucial in providing new insights. Molecular motors are machines that convert free energy, data suggest that during the force-generating confor- mostly obtained from ATP hydrolysis, into mechanical mational change, known as the power stroke, the lever work. The cytoskeletal motor proteins of the myosin and arm of myosins8,11 rotates around its base at the catalytic kinesin families, which interact with actin filaments and domain11–17, which can cause the displacement of bound microtubules, respectively, are the best understood. Less cargo by several nanometres18 (FIG. 1B). In kinesins, the is known about the dynein family of cytoskeletal motors, switching of the neck linker (~13 amino acids connecting which interact with microtubules. Cytoskeletal motors the catalytic core to the cargo-binding stalk domain) from power diverse forms of motility, ranging from the move- an ‘undocked’ state to a state in which it is ‘docked’ to the ment of entire cells (as occurs in muscular contraction catalytic domain, is the equivalent of the myosin power or cell locomotion) to intracellular structural dynamics stroke10. -
Intracellular Transport of Influenza Virus Hemagglutinin to the Apical Surface of Madin-Darby Canine Kidney Cells
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Intracellular Transport of Influenza Virus Hemagglutinin to the Apical Surface of Madin-Darby Canine Kidney Cells ENRIQUE RODRIGUEZ-BOULAN, KEVIN T . PASKIET, PEDRO J. I . SALAS, and ENZO BARD Department of Pathology, Downstate Medical Center, State University of New York, Brooklyn, New York 11203 ABSTRACT The intracellular pathway followed by the influenza virus hemagglutinin (HA) to the apical surface of Madin-Darby canine kidney cells was studied by radioimmunoassay, immunofluorescence, and immunoelectron microscopy. To synchronize the migration, we used a temperature-sensitive mutant of influenza WSN, ts61, which, at the nonpermissive temperature, 39.5°C, exhibits a defect in the HA that prevents its exit from the endoplasmic reticulum . Upon transfer to permissive temperature, 32°C, the HA appeared in the Golgi apparatus after 10 min, and on the apical surface after 30-40 min. In the presence of cycloheximide, the expression was not inhibited, indicating that the is defect is reversible; a wave of HA migrated to the cell surface, where it accumulated with a half time of 60 min . After passage through the Golgi apparatus the HA was detected in a population of smooth vesicles, about twice the size of coated vesicles, located in the apical half of the cytoplasm . These HA-containing vesicles did not react with anti-clathrin antibodies . Monensin (10 'UM) delayed the surface appearance of HA by 2 h, but not the transport to the Golgi apparatus. Incubation at 20°C retarded the migration to the Golgi apparatus by ^-30 min and blocked the surface appearance by acting at a late stage in the intracellular pathway, presumably at the level of the post-Golgi vesicles. -
A Standardized Kinesin Nomenclature • Lawrence Et Al
JCB: COMMENT A standardized kinesin nomenclature Carolyn J. Lawrence,1 R. Kelly Dawe,1,2 Karen R. Christie,3,4 Don W. Cleveland,3,5 Scott C. Dawson,3,6 Sharyn A. Endow,3,7 Lawrence S.B. Goldstein,3,8 Holly V. Goodson,3,9 Nobutaka Hirokawa,3,10 Jonathon Howard,3,11 Russell L. Malmberg,1,3 J. Richard McIntosh,3,12 Harukata Miki,3,10 Timothy J. Mitchison,3,13 Yasushi Okada,3,10 Anireddy S.N. Reddy,3,14 William M. Saxton,3,15 Manfred Schliwa,3,16 Jonathan M. Scholey,3,17 Ronald D. Vale,3,18 Claire E. Walczak,3,19 and Linda Wordeman3,20 1Department of Plant Biology, The University of Georgia, Athens, GA 30602 2Department of Genetics, The University of Georgia, Athens, GA 30602 3These authors contributed equally to this work and are listed alphabetically 4Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305 5Ludwig Institute for Cancer Research, 3080 CMM-East, 9500 Gilman Drive, La Jolla, CA 92093 6Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720 7Department of Cell Biology, Duke University Medical Center, Durham, NC 27710 8Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute, School of Medicine, University of California, San Diego, La Jolla, CA 92093 9Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46628 10Department of Cell Biology and Anatomy, University of Tokyo, Graduate School of Medicine, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan 11Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany 12Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309 13Institute for Chemistry and Cell Biology, Harvard Medical School, Boston, MA 02115 Downloaded from 14Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523 15Department of Biology, Indiana University, Bloomington, IN 47405 16Adolf-Butenandt-Institut, Zellbiologie, University of Munich, Schillerstr. -
Dissertation Kokes M
Mechanisms of Chlamydia Manipulation of Host Cell Biology Revealed Through Genetic Approaches by Marcela Kokes Department of Molecular Genetics and Microbiology Program in Cell and Molecular Biology Duke University Date:_______________________ Approved: ___________________________ Raphael H. Valdivia, Supervisor ___________________________ Daniel J. Lew ___________________________ Jörn Coers ___________________________ Patrick C. Seed Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Molecular Genetics and Microbiology in the Graduate School of Duke University 2015 i v ABSTRACT Mechanisms of Chlamydia Manipulation of Host Cell Biology Revealed Through Genetic Approaches by Marcela Kokes Department of Molecular Genetics and Microbiology Program in Cell and Molecular Biology Duke University Date:_______________________ Approved: ___________________________ Raphael H. Valdivia, Supervisor ___________________________ Daniel J. Lew ___________________________ Jörn Coers ___________________________ Patrick C. Seed An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Molecular Genetics and Microbiology in the Graduate School of Duke University 2015 Copyright by Marcela Kokes 2015 i v Abstract Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen and is the leading cause of preventable blindness worldwide. Chlamydia is particularly intriguing from the perspective of cell biology because it is an obligate intracellular pathogen that manipulates host cellular pathways to ensure its proliferation and survival. This is achieved through a significant remodeling of the host cell’s internal architecture from within a membrane-bound vacuole, termed the inclusion. However, given a previous lack of tools to perform genetic analysis, the mechanisms by which Chlamydia induces host cellular changes remained unclear. -
The Mechanics of Intracellular Transport
Developmental Cell Previews Cutting through the Noise: The Mechanics of Intracellular Transport Samantha Stam1,2 and Margaret L. Gardel2,3,* 1Biophysical Sciences Graduate Program, University of Chicago, Chicago, IL 60637, USA 2James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA 3Department of Physics, University of Chicago, Chicago, IL 60637, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.devcel.2014.08.013 Intracellular transport of organelles and proteins is driven by multiple ATP-dependent processes. Recently in Cell, Guo et al. (2014) developed a technique, force-spectrum microscopy, to measure intracellular forces and demonstrate that large motion of cellular components can be produced by random ATP-dependent fluc- tuations within the cytoplasm. Intracellular transport is crucial to diverse mechanisms, and they overcome the Here, Guo et al. (2014) provide the physiological tasks. The cell employs limitations of diffusive transport in at first measurements to directly charac- multiple mechanisms to meet the de- least two distinct ways. One well-appre- terize these ATP-dependent yet random mands of rapidly transporting cell con- ciated mechanism is that molecular forces within the cytoplasm. The authors tents of varying size over large distances, motor proteins drive directed transport measured the mechanics of the cyto- ranging from microns to up to a meter, to of attached cargo along filament tracks plasm using optical tweezers to apply support specific physiological tasks (Figure 1C, blue and black) (Howard, forces to inert particles microinjected (Figure 1A). In a recent issue of Cell, Guo 2001). Motors transport cargo along into the cytoplasm. -
Chromatography Including Electrophoresis and Other Separation Methods
15SIO 06£ i 36 j 6 VOL. 610 NO.2 JUNE 12, 1992 THIS ISSUE COMPLETES VOL. 610 Bibliography Section JOURNAL OF CHROMATOGRAPHY INCLUDING ELECTROPHORESIS AND OTHER SEPARATION METHODS EDITORS U. A. Th. Brinkman (Amsterdam) R. W. Giese (Boston, MA) J. K. Haken (Kensington, N.S.W.) K. Macek (Prague) L. R. Snyder (Orinda, CA) EDITORS. SYMPOSIUM VOLUMES. E. Heftmann (Orinda. CAl. Z. Deyl (Prague) EDITORIAL BOARD D. W. Armstrong (Rollo. MO) W. A. Aue (Holifo,) P. Botek (8.00) A. A. Boulton (Saskatoon) P. W. Cmr (Minneopolis. MN) N. H. C. Cooke (San Ramon. CAl V. A. Davankov (Moscow) Z. Deyl (Progue) S. Dilli (Kl~nsington. N.S.W.) F. Ern! (Basle) M. B. Evans (Hatfield) J. L. Glojcl, (N. Billerico. MA) G. A. Guiochon (Knoxville, TN) P. R. Haddod (Kensington. N.S.W.) I. M. Hais (Hradec Kralove) W. S. Hancock (San FranCISCo. CAl S. Hjerten (Uppsalo) Cs. Horvinh (New Haven. CT) J. F. K. Huber (Vienna) K.·P. Hupe (Woldbronn) T. W. Hutchens (Houston. IX) J. Jonak (B.oo) P. Jandera (Pardubice) B. L. Kmger (B05<on. MA) J. J. Kirkland (Wilmington. DE) E. sz. Kovats (Lausanne) A. J. P. Mortin (Cambridge) L. W. McLoughlin (Chestnut Hill. MA) E. D. Morgan (Keele) J. O. Pearson (KrJlamazoo, MI) H. Poppe (Amsterdam) F. E. Regnier (West Lafayette. IN) P. G. Righetti (Milan) P. Sclloenmakers (Eindhoven) R. Schwarzenbach (Dubendor!) R. E. Shoup (West Lafayette. IN) A. M. Siouf!i (Mo,seille) D. J. Strydom (Boston. MA) N. Tonaka (Kyoto) S. Terabe (Hyogo) K. K. Unger (Mainz) R. Verpoorle (Leiden) Gy. -
Whole-Genome DNA Methylation Associated with Differentially
Article Whole-Genome DNA Methylation Associated With Differentially Expressed Genes Regulated Anthocyanin Biosynthesis Within Flower Color Chimera of Ornamental Tree Prunus mume Liangbao Jiang 1,2, Man Zhang 1 and Kaifeng Ma 1,* 1 Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing 100083, China; [email protected] (L.J.); [email protected] (M.Z.) 2 School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China * Correspondence: [email protected]; Tel.: +86-10-6233-6321 Received: 19 November 2019; Accepted: 2 January 2020; Published: 10 January 2020 Abstract: DNA methylation is one of the best-studied epigenetic modifications involved in many biological processes. However, little is known about the epigenetic mechanism for flower color chimera of Prunus mume (Japanese apricot, mei). Using bisulfate sequencing and RNA sequencing, we analyzed the white (FBW) and red (FBR) petals collected from an individual tree of Japanese apricot cv. ‘Fuban Tiaozhi’ mei to reveal the different changes in methylation patterns associated with gene expression leading to significant difference in anthocyanins accumulation of FBW (0.012 0.005 mg/g) ± and FBR (0.078 0.013 mg/g). It was found that gene expression levels were positively correlated ± with DNA methylation levels within gene-bodies of FBW and FBR genomes; however, negative correlations between gene expression and DNA methylation levels were detected within promoter domains. In general, the methylation level within methylome of FBW was higher; and in total, 4,618 differentially methylated regions (DMRs) and 1,212 differentially expressed genes (DEGs) were detected from FBW vs. -
S41467-020-16587-W.Pdf
ARTICLE https://doi.org/10.1038/s41467-020-16587-w OPEN Insights into catalysis and regulation of non-canonical ubiquitination and deubiquitination by bacterial deamidase effectors ✉ Yong Wang1,2,4, Qi Zhan1,2,3,4, Xinlu Wang1, Peipei Li1,2,3, Songqing Liu1,2, Guangxia Gao1 & Pu Gao 1,2 The bacterial effector MavC catalyzes non-canonical ubiquitination of host E2 enzyme UBE2N without engaging any of the conventional ubiquitination machinery, thereby abol- 1234567890():,; ishing UBE2N’s function in forming K63-linked ubiquitin (Ub) chains and dampening NF-кB signaling. We now report the structures of MavC in complex with conjugated UBE2N~Ub and an inhibitor protein Lpg2149, as well as the structure of its ortholog, MvcA, bound to Lpg2149. Recognition of UBE2N and Ub depends on several unique features of MavC, which explains the inability of MvcA to catalyze ubiquitination. Unexpectedly, MavC and MvcA also possess deubiquitinase activity against MavC-mediated ubiquitination, highlighting MavC as a unique enzyme possessing deamidation, ubiquitination, and deubiquitination activities. Further, Lpg2149 directly binds and inhibits both MavC and MvcA by disrupting the inter- actions between enzymes and Ub. These results provide detailed insights into catalysis and regulation of MavC-type enzymes and the molecular mechanisms of this non-canonical ubiquitination machinery. 1 CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. 2 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. 3 University ✉ of Chinese Academy of Sciences, Beijing 100049, China. 4These authors contributed equally: Yong Wang, Qi Zhan.