Construction and Loss of Bacterial Flagellar Filaments
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Motility in Prokaryotes O Bacterial Flagella O Gliding Motility O Chemosensing · Movement of Materials Within Bacteria and Cell Size · Magnetotactic Bactertia
Biology of the Prokaryotes The following is a series of essays on selected aspects of prokaryote biology. These essays are ongoing, and the references are periodically updated, so do not assume completion (not that such works can ever be complete). The following topics are covered: · Motility in Prokaryotes o Bacterial flagella o Gliding motility o Chemosensing · Movement of materials within bacteria and cell size · Magnetotactic bactertia Motility in Prokaryotes 1. Motility Mode 1 - Bacterial Flagella 1.1 Introduction Some bacteria are non-motile, relying entirely upon passive flotation and Brownian motion for dispersal. However, most are motile; at least during some stage of their lifecycle. Motile bacteria move with "intent", gathering in regions which are hot or cold, light or dark, or of favourable chemical/nutrient content. This is obviously a useful attribute. Many species glide across the substratum. This may involve specific organelles, such as the filament bearing goblet-shaped structures in the walls of Flexibacter (Moat, 1979). Often, however, no specific organelles appear to be involved and gliding may be attributable to the slime covering of some bacteria or the streaming of outer membrane lipids of others (e.g. Cytophaga (Moat, 1979)) or to other mechanisms currently being elucidated (see section 2). The spiral-shaped Spiroplasma corkscrews its way through the medium by means of membrane-associated fibrils resembling eukaryotic actin (Boyd, 1988). Gonogoocci exhibit twitching motility (intermittent, jerky movements) due to the presence of pili (fine filaments, 7 nm diameter, less than one micrometer long) which branch and rejoin to form an irregular surface lattice. However, more than half of motile bacteria use one or more helical, whip-like appendages, about 24 nm diameter and up to 10 mm long, called flagella (sing. -
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]. -
Chloroplast Transit Peptides: Structure, Function and Evolution
reviews Chloroplast transit Although the first demonstration of precursor trans- port into chloroplasts was shown over two decades peptides: structure, ago3,4, only now is this area of cell biology becom- ing well understood. Many excellent reviews have been published recently on the evolution of plas- function and tids5, the evolution of organelle genomes6, the mechanism of gene transfer from organelles to the nucleus7 and the mechanism of protein import into evolution chloroplasts8,9. Proteins destined to plastids and other organ- elles share in common the requirement for ‘new’ Barry D. Bruce sequence information to facilitate their correct trafficking within the cell. Although in most cases this information resides in a cleavable, N-terminal sequence often collectively referred to as signal It is thought that two to three thousand different proteins are sequence, the different organelle-targeting se- targeted to the chloroplast, and the ‘transit peptides’ that act as quences have distinct properties and names: ‘signal peptides’ for the endoplasmic reticulum, chloroplast targeting sequences are probably the largest class of ‘presequences’ for the mitochondria and ‘transit peptides’ for chloroplasts and other plastids. This targeting sequences in plants. At a primary structural level, transit review focuses on recent progress in dissecting peptide sequences are highly divergent in length, composition and the role of the stromal-targeting domain of chloro- plast transit peptides. I will consider briefly the organization. An emerging concept suggests that transit peptides multitude of distinct functions that transit peptides contain multiple domains that provide either distinct or overlapping perform, provide an update on the limited struc- tural information of a number of transit peptides functions. -
Bacterial Cell Membrane
BACTERIAL CELL MEMBRANE Dr. Rakesh Sharda Department of Veterinary Microbiology NDVSU College of Veterinary Sc. & A.H., MHOW CYTOPLASMIC MEMBRANE ➢The cytoplasmic membrane, also called a cell membrane or plasma membrane, is about 7 nanometers (nm; 1/1,000,000,000 m) thick. ➢It lies internal to the cell wall and encloses the cytoplasm of the bacterium. ➢It is the most dynamic structure of a prokaryotic cell. Structure of cell membrane ➢The structure of bacterial plasma membrane is that of unit membrane, i.e., a fluid phospholipid bilayer, composed of phospholipids (40%) and peripheral and integral proteins (60%) molecules. ➢The phospholipids of bacterial cell membranes do not contain sterols as in eukaryotes, but instead consist of saturated or monounsaturated fatty acids (rarely, polyunsaturated fatty acids). ➢Many bacteria contain sterol-like molecules called hopanoids. ➢The hopanoids most likely stabilize the bacterial cytoplasmic membrane. ➢The phospholipids are amphoteric molecules with a polar hydrophilic glycerol "head" attached via an ester bond to two non-polar hydrophobic fatty acid tails. ➢The phospholipid bilayer is arranged such that the polar ends of the molecules form the outermost and innermost surface of the membrane while the non-polar ends form the center of the membrane Fluid mosaic model ➢The plasma membrane contains proteins, sugars, and other lipids in addition to the phospholipids. ➢The model that describes the arrangement of these substances in lipid bilayer is called the fluid mosaic model ➢Dispersed within the bilayer are various structural and enzymatic proteins, which carry out most membrane functions. ➢Some membrane proteins are located and function on one side or another of the membrane (peripheral proteins). -
하구 및 연안생태학 Estuarine and Coastal Ecology
하구 및 연안생태학 Estuarine and coastal ecology 2010 년 11월 2 계절적 변동 • 빛과 영양염분의 조건에 따라 • 봄 가을 대발생 계절적 변동 Sverdrup 에 의한 대발생 모델 • Compensation depth (보상심도) • Critical depth (임계수심) Sverdrup 에 의한 대발생 모델 홍재상외, 해양생물학 Sverdrup 에 의한 대발생 모델 봄 여름 가을 겨울 수심 혼합수심 임계수심 (mixed layer depth) (critical depth) Sverdrup 에 의한 대발생 모델 봄 여름 가을 겨울 수심 혼합수심 임계수심 (mixed layer depth) (critical depth) Diatoms (규조류) • Bacillariophyceae (1 fragment of centrics, 19 fragments of pennates in Devonian marble in Poland Kwiecinska & Sieminska 1974) Diatoms (규조류) • Bacillariophyceae • Temperate and high latitude (everywhere) Motility: present in pennate diatoms with a raphe (and male gametes) Resting cells (spores): heavily silicified, often with spines (Î보충설명) Biotopes: marine and freshwater, plankton, benthos, epiphytic, epizooic (e.g., on whales, crustaceans) endozoic, endophytic, discolouration of arctic and Antarctic sea ice Snow Algae (규조류 아님) Snow algae describes cold-tolerant algae and cyanobacteria that grow on snow and ice during alpine and polar summers. Visible algae blooms may be called red snow or watermelon snow. These extremophilic organisms are studied to understand the glacial ecosystem. Snow algae have been described in the Arctic, on Arctic sea ice, and in Greenland, the Antarctic, Alaska, the west coast, east coast, and continental divide of North America, the Himalayas, Japan, New Guinea, Europe (Alps, Scandinavia and Carpathians), China, Patagonia, Chile, and the South Orkney Islands. Diatoms (규조류) • Bacillariophyceae • Temperate and high latitude (everywhere) • 2~1000 um • siliceous frustules • Various patterns in frustule Centric vs Pennate Centric diatom Pennete small discoid plastid large plate plastid Navicula sp. -
Flagellum Couples Cell Shape to Motility in Trypanosoma Brucei
Flagellum couples cell shape to motility in Trypanosoma brucei Stella Y. Suna,b,c, Jason T. Kaelberd, Muyuan Chene, Xiaoduo Dongf, Yasaman Nematbakhshg, Jian Shih, Matthew Doughertye, Chwee Teck Limf,g, Michael F. Schmidc, Wah Chiua,b,c,1, and Cynthia Y. Hef,h,1 aDepartment of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305; bDepartment of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA 94305; cSLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; dDepartment of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030; eVerna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030; fMechanobiology Institute, National University of Singapore, Singapore 117411; gDepartment of Mechanical Engineering, National University of Singapore, Singapore 117575; and hDepartment of Biological Sciences, Center for BioImaging Sciences, National University of Singapore, Singapore 117543 Contributed by Wah Chiu, May 17, 2018 (sent for review December 29, 2017; reviewed by Phillipe Bastin and Abraham J. Koster) In the unicellular parasite Trypanosoma brucei, the causative Cryo-electron tomography (cryo-ET) allows us to view 3D agent of human African sleeping sickness, complex swimming be- supramolecular details of biological samples preserved in their havior is driven by a flagellum laterally attached to the long and proper cellular context without chemical fixative and/or metal slender cell body. Using microfluidic assays, we demonstrated that stain. However, samples thicker than 1 μm are not accessible to T. brucei can penetrate through an orifice smaller than its maxi- cryo-ET because at typical accelerating voltages (≤300 kV), few mum diameter. -
Patterns of Bacterial Diversity in the Marine Planktonic Particulate Matter Continuum
The ISME Journal (2017) 11, 999–1010 © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Patterns of bacterial diversity in the marine planktonic particulate matter continuum Mireia Mestre, Encarna Borrull, M Montserrat Sala and Josep M Gasol Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Barcelona, Catalunya, Spain Depending on their relationship with the pelagic particulate matter, planktonic prokaryotes have traditionally been classified into two types of communities: free-living (FL) or attached (ATT) to particles, and are generally separated using only one pore-size filter in a differential filtration. Nonetheless, particulate matter in the oceans appears in a continuum of sizes. Here we separated this continuum into six discrete size-fractions, from 0.2 to 200 μm, and described the prokaryotes associated to each of them. Each size-fraction presented different bacterial communities, with a range of 23–42% of unique (OTUs) in each size-fraction, supporting the idea that they contained distinct types of particles. An increase in richness was observed from the smallest to the largest size- fractions, suggesting that increasingly larger particles contributed new niches. Our results show that a multiple size-fractionation provides a more exhaustive description of the bacterial diversity and community structure than the use of only one filter. In addition, and based on our results, we propose an alternative to the dichotomy of FL or ATT lifestyles, in which we differentiate the taxonomic groups with preference for the smaller fractions, those that do not show preferences for small or large fractions, and those that preferentially appear in larger fractions. -
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. -
Cell Membrane
John Lenyo Corrina Perez Hazel Owens Cell Membrane http://micro.magnet.fsu.edu/cells/plasmamembrane/plasmamembrane.html • Cell membranes are composed of proteins and lipids. • Since they are made up of mostly lipids, only certain substances can move through. spmbiology403.blogspot.com •Phospholipids are the most abundant type of lipid found in the membrane. Phospholipids are made up of two layers, the outer and inner layers. The inside layer is made of hydrophobic fatty acid tails, while the outer layer is made up of hydrophilic polar heads that are pointed toward the water. academic.brooklyn.cuny.edu •Membrane structure relies on the tendency of fatty acid molecules to spread on the surface of water. • Membrane proteins (which take up half of the membrane) determine what gets into and leaves the cell. •Glycolipids are found on the outer part of the cell membrane. Single Chain vs. Phospholipid • Single chain lipids were assumed to be the first of those to form cell membranes with the more complex phospholipids evolving later • Phospholipids can be synthesized in an abiotic environment without enzymes now • Phosphoplipid bilayers now make up the plasma cell membranes that regulate movement into and out of prokaryotic and eukaryotic cells. Single chain lipid http://web.nestucca.k12.or.us/nvhs/staff/whitehead/homewor http://clincancerres.aacrjournals.org/content/11/5/2018/F1. k.htm expansion Types of Lipids • Today Plasma Membranes are made primarily of phospholipids • It is thought that early membranes may have been made of simpler fatty acids. http://exploringorigins.org/fattyacids.html Properties of Fatty Acids • They are Ampipathic, meaning that they have a hydrophobic (“water hating”) end and a hydrophilic (water loving”) end. -
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. -
Cell Wall Constrains Lateral Diffusion of Plant Plasma-Membrane Proteins
Cell wall constrains lateral diffusion of plant SEE COMMENTARY plasma-membrane proteins Alexandre Martinièrea, Irene Lavagia, Gayathri Nageswarana, Daniel J. Rolfeb, Lilly Maneta-Peyretc, Doan-Trung Luud, Stanley W. Botchwayb, Stephen E. D. Webbb, Sebastien Mongrandc, Christophe Maureld, Marisa L. Martin-Fernandezb, Jürgen Kleine-Vehne, Jirí Frimlf, Patrick Moreauc, and John Runionsa,1 aDepartment of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom; bCentral Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Oxfordshire OX11 0QX, United Kingdom; cLaboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200 Centre National de la Recherche Scientifique, Université Bordeaux Segalen, 33076 Bordeaux, France; dLaboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, Unité Mixte de Recherche 5004, Centre National de la Recherche Scientifique/Unité Mixte de Recherche 0386 Institut National de la Recherche Agronomique, 34060 Montpellier, France; eDepartment of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; and fDepartment of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium Edited by Daniel J. Cosgrove, Pennsylvania State University, University Park, PA, and approved May 16, 2012 (received for review February 3, 2012) A cell membrane can be considered a liquid-phase plane in which yeast lines lacking -
Control of Molecular Motor Motility in Electrical Devices
Control of Molecular Motor Motility in Electrical Devices Thesis submitted in accordance with the requirements of The University of Liverpool for the degree of Doctor in Philosophy By Laurence Charles Ramsey Department of Electrical Engineering & Electronics April 2014 i Abstract In the last decade there has been increased interest in the study of molecular motors. Motor proteins in particular have gained a large following due to their high efficiency of force generation and the ability to incorporate the motors into linear device designs. Much of the recent research centres on using these protein systems to transport cargo around the surface of a device. The studies carried out in this thesis aim to investigate the use of molecular motors in lab- on-a-chip devices. Two distinct motor protein systems are used to show the viability of utilising these nanoscale machines as a highly specific and controllable method of transporting molecules around the surface of a lab-on-a-chip device. Improved reaction kinetics and increased detection sensitivity are just two advantages that could be achieved if a motor protein system could be incorporated and appropriately controlled within a device such as an immunoassay or microarray technologies. The first study focuses on the motor protein system Kinesin. This highly processive motor is able to propel microtubules across a surface and has shown promise as an in vitro nanoscale transport system. A novel device design is presented where the motility of microtubules is controlled using the combination of a structured surface and a thermoresponsive polymer. Both topographic confinement of the motility and the creation of localised ‘gates’ are used to show a method for the control and guidance of microtubules.