Chapter 4 – Cell Structure
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The Nature of Genomes Viral Genomes Prokaryotic Genome
The nature of genomes • Genomics: study of structure and function of genomes • Genome size – variable, by orders of magnitude – number of genes roughly proportional to genome size • Plasmids – symbiotic DNA molecules, not essential – mostly circular in prokaryotes • Organellar DNA – chloroplast, mitochondrion – derived by endosymbiosis from bacterial ancestors Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Viral genomes • Nonliving particle In prokaryotes, viruses are – nucleic acid sometimes referred to as – protein bacteriophages. • DNA or RNA – single-stranded or double-stranded – linear or circular • Compact genomes with little spacer DNA Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Prokaryotic genome • Usually circular double helix – occupies nucleoid region of cell – attached to plasma membrane • Genes are close together with little intergenic spacer • Operon – tandem cluster of coordinately regulated genes – transcribed as single mRNA • Introns very rare Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company Chapter 2: Genes and genomes © 2002 by W. H. Freeman and Company 1 Eukaryotic nuclear genomes • Each species has characteristic chromosome number • Genes are segments of nuclear chromosomes • Ploidy refers to number of complete sets of chromosomes –haploid (1n): one complete set of genes – diploid (2n) – polyploid (≥3n) • In diploids, chromosomes come in homologous pairs (homologs) In humans, somatic cells have – structurally similar 2n = 46 chromosomes. – same sequence of genes – may contain different alleles Chapter 2: Genes and genomes © 2002 by W. H. -
Diversity of Plant Virus Movement Proteins: What Do They Have in Common?
processes Review Diversity of Plant Virus Movement Proteins: What Do They Have in Common? Yuri L. Dorokhov 1,2,* , Ekaterina V. Sheshukova 1, Tatiana E. Byalik 3 and Tatiana V. Komarova 1,2 1 Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; [email protected] (E.V.S.); [email protected] (T.V.K.) 2 Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia 3 Department of Oncology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; [email protected] * Correspondence: [email protected] Received: 11 November 2020; Accepted: 24 November 2020; Published: 26 November 2020 Abstract: The modern view of the mechanism of intercellular movement of viruses is based largely on data from the study of the tobacco mosaic virus (TMV) 30-kDa movement protein (MP). The discovered properties and abilities of TMV MP, namely, (a) in vitro binding of single-stranded RNA in a non-sequence-specific manner, (b) participation in the intracellular trafficking of genomic RNA to the plasmodesmata (Pd), and (c) localization in Pd and enhancement of Pd permeability, have been used as a reference in the search and analysis of candidate proteins from other plant viruses. Nevertheless, although almost four decades have passed since the introduction of the term “movement protein” into scientific circulation, the mechanism underlying its function remains unclear. It is unclear why, despite the absence of homology, different MPs are able to functionally replace each other in trans-complementation tests. Here, we consider the complexity and contradictions of the approaches for assessment of the ability of plant viral proteins to perform their movement function. -
Development and Function of Plasmodesmata in Zygotes of Fucus Distichus
Botanica Marina 2015; 58(3): 229–238 Chikako Nagasato*, Makoto Terauchi, Atsuko Tanaka and Taizo Motomura Development and function of plasmodesmata in zygotes of Fucus distichus Abstract: Brown algae have plasmodesmata, tiny tubu- Introduction lar cytoplasmic channels connecting adjacent cells. The lumen of plasmodesmata is 10–20 nm wide, and it takes a Multicellular organisms such as animals, fungi, land simple form, without a desmotubule (the inner membrane plants, and brown algae have specific cellular connections. structure consisting of endoplasmic reticulum in the plas- These structures connect the cytoplasm of adjacent cells modesmata of green plants). In this study, we analyzed and provide a route for cell-cell communication. Green the ultrastructure and distribution of plasmodesmata plants, including land plants and certain species of green during development of Fucus distichus zygotes. The first algae (reviewed in Robards and Lucas 1990, Raven 1997), cytokinesis of zygotes in brown algae is not accompanied and brown algae (Bisalputra 1966) possess plasmodes- by plasmodesmata formation. As the germlings develop, mata. These are cytoplasmic canals that pass through the plasmodesmata are found in all septal cell walls, includ- septal cell wall and connect adjacent cells. Plasmodes- ing the first cell division plane. Plasmodesmata are formed mata in green plants and brown algae share similar char- de novo on the existing cell wall. Pit fields, which are clus- acteristics; however, plasmodesmata in brown algae lack ters of plasmodesmata, were observed in germlings with a desmotubule, a tubular strand of connecting endoplas- differentiated cell layers. Apart from the normal plas- mic reticulum (ER) that penetrates the plasmodesmata modesmata, these pit fields had branched plasmodes- of land plants (Terauchi et al. -
The Mitochondrial Genome. the Nucleoid
ISSN 0006-2979, Biochemistry (Moscow), 2016, Vol. 81, No. 10, pp. 1057-1065. © Pleiades Publishing, Ltd., 2016. Original Russian Text © A. A. Kolesnikov, 2016, published in Biokhimiya, 2016, Vol. 81, No. 10, pp. 1322-1331. REVIEW The Mitochondrial Genome. The Nucleoid A. A. Kolesnikov Lomonosov Moscow State University, Faculty of Biology, 119991 Moscow, Russia; E-mail: [email protected] Received May 30, 2016 Revision received July 1, 2016 Abstract—Mitochondrial DNA (mtDNA) in cells is organized in nucleoids containing DNA and various proteins. This review discusses questions of organization and structural dynamics of nucleoids as well as their protein components. The structures of mt-nucleoid from different organisms are compared. The currently accepted model of nucleoid organization is described and questions needing answers for better understanding of the fine mechanisms of the mitochondrial genetic apparatus functioning are discussed. DOI: 10.1134/S0006297916100047 Key words: mitochondrial nucleoid, mitochondrial genome It is now clear that understanding of genome organ- mtDNA). In fact, proteins associated with a nucleoid can ization of subcellular structures is necessary for under- influence the speed of accumulation of mutations. standing of cellular processes occurring through the cell In the last decade, reviews devoted to this subject cycle, including questions of storage, realization, and appeared regularly [5-9]. Generally, they cover the subject transmission of genetic information. A considerable of nucleoid organization in metazoan mitochondria amount of information about forms and sizes of mito- (mainly in human cells) and fungi (mainly yeast). chondrial DNA (mtDNA) throughout evolution has been Reviews touching plant cells are much less frequent [10, accumulated [1]. -
Basic Features of All Cells
Plasma Lab 4 membrane Basic Semifluid Ribosomes features substance (make called proteins) of all cytosol cells Chromosomes (carry genes) © 2014 Pearson Education, Inc. Prokaryotic cells are characterized by having . No nucleus . DNA in an unbound region called the nucleoid . No membrane-bound organelles . Cytoplasm bound by the plasma membrane © 2014 Pearson Education, Inc. Eukaryotic cells are characterized by having • DNA in a nucleus that is bounded by a membranous nuclear envelope • Membrane-bound organelles • Cytoplasm in the region between the plasma membrane and nucleus Eukaryotic cells are generally much larger than prokaryotic cells © 2014 Pearson Education, Inc. Figure 6.8a ENDOPLASMIC RETICULUM (ER) Nuclear envelope Rough ER Smooth ER Nucleolus NUCLEUS Flagellum Chromatin Centrosome Plasma membrane CYTOSKELETON: Microfilaments Intermediate filaments Microtubules Ribosomes Microvilli Golgi apparatus Peroxisome Lysosome Mitochondrion © 2014 Pearson Education, Inc. Figure 6.8b Nuclear envelope NUCLEUS Nucleolus Rough ER Chromatin Smooth ER Ribosomes Golgi Central vacuole apparatus Microfilaments CYTOSKELETON Microtubules Mitochondrion Peroxisome Plasma Chloroplast membrane Cell wall Plasmodesmata Wall of adjacent cell © 2014 Pearson Education, Inc. © 2014 Pearson Education, Inc. © 2014 Pearson Education, Inc. © 2014 Pearson Education, Inc. Table 6.1 © 2014 Pearson Education, Inc. Cell Walls of Plants The cell wall is an extracellular structure that distinguishes plant cells from animal cells Plant cell walls Prokaryotes, are made -
Coli Chromosome Into a Nucleoid Filament
Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament Paul A. Wigginsa,1, Keith C. Cheverallsa,b, Joshua S. Martina,b, Robert Lintnera, and Jané Kondevb aWhitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142; and bMartin A. Fisher School of Physics, Brandeis University, 415 South Street, Waltham, MA 02453 Edited by Nancy E Kleckner, Harvard University, Cambridge, MA, and approved January 27, 2010 (received for review October 26, 2009) The stochasticity of chromosome organization was investigated by Our quantitative measurements of E. coli nucleoid structure con- fluorescently labeling genetic loci in live Escherichia coli cells. In firm this qualitative picture: The body of the nucleoid is linearly spite of the common assumption that the chromosome is well organized along the long-axis of the cell, implying that the modeled by an unstructured polymer, measurements of the locus nucleoid has a nearly-constant linear packing density, except distributions reveal that the E. coli chromosome is precisely orga- for a short region, genomically ter-proximate, which connects nized into a nucleoid filament with a linear order. Loci in the body the two arms of the chromosome (11). But in spite of the obser- of the nucleoid show a precision of positioning within the cell of vation of a linear chromosome organization in both E. coli and better than 10% of the cell length. The precision of interlocus dis- C. crescentus, the mechanism which gives rise to this characteristic tance of genomically-proximate loci was better than 4% of the cell structure is unknown. length. The measured dependence of the precision of interlocus To probe the mechanism of nucleoid organization, we measure distance on genomic distance singles out intranucleoid interactions and analyze the position fluctuations of single loci and the cor- as the mechanism responsible for chromosome organization. -
The Chloroplast Nucleoid in Ochromonas Danica I
J. Cell Sci. 16, 557-577 0974) 557 Printed in Great Britain THE CHLOROPLAST NUCLEOID IN OCHROMONAS DANICA I. THREE-DIMENSIONAL MORPHOLOGY IN LIGHT- AND DARK-GROWN CELLS SARAH P. GIBBS, D. CHENG AND T. SLANKIS Department of Biology, McGill University, Montreal HT,C 3G1, Canada SUMMARY The 3-dimensional structure of the plastid nucleoid was determined from serial sections of the plastid of dark-grown, greening, and light-grown cells of Ochromonas danica. In light- grown and greening cells, the chloroplast nucleoid forms a continuous cord or ring which closely follows the rim of each lateral lobe of the chloroplast and is continuous across the top and bottom of the bridge connecting the 2 chloroplast lobes. The nucleoid always lies just inside the chloroplast girdle bands where they loop around the rim of the plastid. It was demonstrated by electron-microscopic autoradiography of greening cells labelled with [3H]- thymidine that all the plastid DNA is localized in this peripheral ring-shaped nucleoid. In the proplastid of dark-grown cells, the nucleoid also forms a ring-shaped structure lying just inside the single girdle thylakoid, although frequent irregularities, such as gaps, are present. It is postulated that the girdle bands determine the shape of the chloroplast nucleoid, possibly by having specific attachment sites for the plastid DNA molecules. A survey of the literature shows that a peripheral ring-shaped chloroplast nucleoid is a characteristic feature of the 5 classes of algae whose chloroplasts possess girdle bands, namely the Raphidophyceae, Chryso- phyceae, Bacillariophyceae, Xanthophyceae, and Phaeophyceae, and has never been observed in plants whose plastids lack girdle bands. -
In Situ Imaging of Mitochondrial Translation Shows Weak Correlation
© 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 4193-4199 doi:10.1242/jcs.206714 TOOLS AND RESOURCES In situ imaging of mitochondrial translation shows weak correlation with nucleoid DNA intensity and no suppression during mitosis Christopher Estell1, Emmanouela Stamatidou2, Sarah El-Messeiry2,3 and Andrew Hamilton2,* ABSTRACT not been tested because no method exists to examine total de novo Although mitochondrial translation produces only 13 proteins, we show mitochondrial genome and expression simultaneously in situ here how this process can be visualised and detected in situ . Mitochondrial genome polymorphisms (heteroplasmy) is by fluorescence microscopy with a simple, rapid and inexpensive also common in mammalian cells (Larsson, 2010; He et al., 2010), procedure using non-canonical amino acid labelling and click partly due to the much higher mutation rate of mitochondrial DNA chemistry. This allows visualisation of the translational output in compared to nuclear DNA (Taylor et al., 2003) but, again, it is not different mitochondria within a cell, their position within that cell and a known how such sequence variation affects overall genome comparison of mitochondrial translation between cells. The most highly expression. Heterogeneity of mitochondrial membrane potential translationally active mitochondria were closest to the nucleus but were and activity of some mitochondrial enzymes have been observed also found at the distal end of long cellular projections. There were and associated with disease (Wikstrom et al., 2009), in a way similar substantial differences in translation between adjacent mitochondria to that of genetic polymorphism. However, the extent to which and this did not readily correlate with apparent mitochondrial genome such physiological heterogeneity arises from mitochondrial gene content. -
Microgametophytic Plastid Nucleoid Content and Reproductive and Life History Traits of Tribe Trifolieae (Fabaceae)
Plant P1. Syst. Evol. 196:89-98 (1995) Systematics and Evolution '© Springer-Verlag 1995 Printed in Austria Microgametophytic plastid nucleoid content and reproductive and life history traits of tribe Trifolieae (Fabaceae) R. N. KEYS, S. E. SMITH, H. LLOYD MOOENSEN, and E. SMALL Received August 2, 1994; in revised version September 28, 1994 Key words: Leguminosae, Medicago, alfalfa. - Microgametophyte, biparental inheri- tance, DAPI. Abstract: Microgametophytic plastid nucleoids were quantified for 18 species represent- ing the four core genera of the tribe Trifolieae (Fabaceae), Medicago, Melilotus, Trigonel- la, and Trifolium. Generative cells of all taxa contained nucleoids, establishing that bipa- rental plastid inheritance is common in the Trifolieae. Nucleoid number and volumes of pollen grains and generative cell nuclei differed among taxa. Nucleoid number was posi- tively correlated with pollen grain and generative cell nuclear volumes, flower size and style length. These relationships disappeared after adjusting nucleoid number for pollen grain and generative cell nuclear volumes. Adjusted nucleoid numbers provided no evi- dence to support hypotheses that plastid content is associated with ploidy level, mating system, perenniality or size of the reproductive apparatus. Advances in cytology and molecular biology have stimulated interest in describ- ing the mode of organelle inheritance in plants. Data from a number of studies have shown that the assumption of strict maternal inheritance of plastids in angio- sperms is not justified (review in HARRIS • INGRAM 1991). Using the DNA fluo- rochrome DAPI (4'-6-diamidino-2-phenylindole), CORRIVEAU & COLEMAN (1988) analyzed generative or sperm cells from 235 angiosperm species for the presence of plastid nucleoids (DNA aggregates) and found cytological evidence for poten- tial paternal inheritance of plastids in 43 species from 26 genera. -
Plasmodesmata and the Control of Symplastic Transport
Blackwell Science, LtdOxford, UKPCEPlant, Cell and Environment0016-8025Blackwell Publishing Ltd 2002 26 Original Article Plant, Cell and Environment (2003) 26, 103–124 Plasmodesmata and the control of symplastic transport A. G. ROBERTS & K. J. OPARKA Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK ‘There are holes in the sky other cells, some degree of intercellular connection is main- where the rain gets in, tained. This plasmodesmal continuum that potentially but they’re ever so small exists throughout the whole plant is termed the symplast that’s why rain’s so thin’ (Münch 1930). However, the symplast is not the open con- Spike Milligan (1968) tinuum that Münch originally hypothesized, but is divided into functional domains, each tightly regulated by different In 1879 Eduard Tangle discovered cytoplasmic connections forms of plasmodesmata (Erwee & Goodwin 1985; Ehlers between cells in the cotyledons of Strychnos nuxvomica, & Kollmann 2001). Plasmodesmata are now thought of as which he interpreted to be protoplasmic contacts. This led fluid, dynamic structures that can be modified both struc- him to hypothesize that ‘the protoplasmic bodies . are turally and functionally to cope with the requirements of united by thin strands passing through connecting ducts in specific cells and tissues. the walls, which put the cells into connection with each other and so unite them to an entity of higher order’ (Carr 1976). This challenged the then current view that cells func- THE STRUCTURE OF PLASMODESMATA tioned as autonomous units. It was after much research in Based on structure, two basic types of plasmodesmata have many other species and cell types that Strasburger, in 1901, been characterized; simple and branched. -
Tobacco Mosaic Virus Movement Protein Associates with the Cytoskeleton in Tobacco Cells
The Plant Cell, Vol. 7, 2101-21 14, December 1995 O 1995 American Society of Plant Physiologists Tobacco Mosaic Virus Movement Protein Associates with the Cytoskeleton in Tobacco Cells 8. Gail McLean, John Zupan, and Patricia C. Zambryskil Department of Plant Biology, University of California-Berkeley, Berkeley, California 94720-3102 Tobacco mosaic virus movement protein P30 complexes with genomic viral RNA for transport through plasmodesmata, the plant intercellular connections. Although most research with P30 focuses on its targeting to and gating of plasmodes- mata, the mechanisms of P30 intracellularmovement to plasmodesmata have not been defined. To examine P30 intracellular localization, we used tobacco protoplasts, which lack plasmodesmata, for transfection with plasmids carrying P30 cod- ing sequences under a constitutive promoter and for infection with tobacco mosaic virus particles. In both systems, P30 appears as filaments that colocalize primarily with microtubules. To a lesser extent, P30 filaments colocalize with actin filaments, and in vitro experiments suggested that P30 can bind directly to actin and tubulin. This association of P30 with cytoskeletal elements may play a critical role in intracellular transport of the P30-vira1 RNA complex through the cytoplasm to and possibly through plasmodesmata. INTRODUCTION To establish a systemic infection, plant viruses must move from that the cytoskeleton acts as a trafficking system for intracel- the infection site to the rest of the plant. For many plant viruses, lular transport, translocating vesicles, organelles, protein, and a virus-encoded product, the movement protein, actively poten- even mRNA to specific cellular locations (Williamson, 1986; tiates viral cell-to-cell spread through plasmodesmata, the Vale, 1987; Dingwall, 1992; Singer, 1992; Wilhelm and Vale, cytoplasmic bridges that function as intercellular connections 1993; Bassell et al., 1994; Hesketh, 1994). -
Organelle–Nucleus Cross-Talk Regulates Plant Intercellular
Organelle–nucleus cross-talk regulates plant PNAS PLUS intercellular communication via plasmodesmata Tessa M. Burch-Smitha, Jacob O. Brunkarda, Yoon Gi Choib, and Patricia C. Zambryskia,1 aDepartment of Plant and Microbial Biology and bFunctional Genomics Laboratory, University of California, Berkeley, CA 94720 Contributed by Patricia C. Zambryski, October 19, 2011 (sent for review June 20, 2011) We use Arabidopsis thaliana embryogenesis as a model system by either depositing or removing callose from the cell walls sur- for studying intercellular transport via plasmodesmata (PD). A rounding PD openings. PD also contain cytoskeleton-associated forward genetic screen for altered PD transport identified in- proteins, including actin (7) and myosin (8). Proteins with potential creased size exclusion limit (ise) 1 and ise2 mutants with increased roles in signal transduction are also PD constituents, such as a intercellular transport of fluorescent 10-kDa tracers. Both ise1 and calcium kinase (9), calreticulin (10), a kinase that phosphorylates ise2 exhibit increased formation of twinned and branched PD. viral movement proteins (11), and membrane receptor-like pro- ISE1 encodes a mitochondrial DEAD-box RNA helicase, whereas teins [PD-localized proteins (PDLPs)] (12). Remorin, a lipid-raft ISE2 encodes a DEVH-type RNA helicase. Here, we show that protein, was also recently found to localize to PD (13). Several ISE2 foci are localized to the chloroplast stroma. Surprisingly, additional potential membrane-bound PD-localized proteins have ise1 ise2 plastid development is defective in both and mutant recently been reported (14). embryos. In an effort to understand how RNA helicases that lo- We conducted a genetic screen of embryo-lethal mutants to calize to different organelles have similar impacts on plastid and identify genes critical to regulating PD function (15).