DOCSLIB.ORG

Colocalization of Distant Chromosomal Loci in Space in E. Coli: a Bacterial Nucleolus

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Colocalization of Distant Chromosomal Loci in Space in E. Coli: a Bacterial Nucleolus Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus Tamas Gaal,1 Benjamin P. Bratton,2 Patricia Sanchez-Vazquez,1 Alexander Sliwicki,1 Kristine Sliwicki,1 Andrew Vegel,1 Rachel Pannu,1 and Richard L. Gourse1 1Department of Bacteriology, 2Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome orga- nization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180° on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA op- eron pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus. [Keywords: bacterial chromosome structure; rRNA operons; nucleolus; long-distance chromosomal interactions; ParB-CFP and YFP fusions] Supplemental material is available for this article. Received September 5, 2016; revised version accepted October 5, 2016. The Escherichia coli chromosome is a single ∼4.6-mil- connected by an elongated ter region (Wang et al. 2006; lion-base-pair (bp) circular DNA molecule with a contour Wiggins et al. 2010). In a second model, the left and right length of ∼1.5 mm, ∼1000-fold longer than the bacterial arms of the chromosome are folded together with oriC at cell. One operon of ∼5 kb (the length of a ribosomal one end and ter at the other end of the filament (Youngren RNA [rRNA] operon) in theory could stretch the entire et al. 2014). In a third model, the chromosome is organized length of the bacterial cell if it were present as B-form into four macrodomains and two nonstructured regions DNA without compaction. How the chromosome is com- with a locus able to interact only with another locus in pacted and folded to form the bacterial nucleoid has been the same macrodomain or with a locus in the nonstruc- the subject of intense investigation in recent years, in part tured regions, resulting in genetic and spatial separation because it has implications for genome integrity, cell divi- between different partsof thechromosome (Espéli andBoc- sion, gene expression, and antibiotic resistance. card 2006; Espeli et al. 2008). The models are not mutually Unlike the eukaryotic nucleus, the bacterial nucleoid is exclusive, and certain models could be more applicable to not physically separated from the cytoplasm by a mem- certain times, growth conditions, or bacterial species. brane. However, like the eukaryotic chromosome, the How specific DNA loci are arranged within these broad bacterial chromosome appears to be highly organized, general outlines remains to be determined. The positions changes with the cell cycle, and responds to nutritional of individual loci in space are dynamic (Espeli et al. 2008), conditions (Thanbichler and Shapiro 2006; Dorman but systematic, genome-wide cytological analyses of both 2013; Jin et al. 2013; Dame and Tark-Dame 2016). This the E. coli and Caulobacter crescentus chromosomes con- has led to characterizations of the nucleoid as a complex cluded that the linear order of genes in space recapitulates and evolving but coherent object whose intrinsic mechan- the genetic map (Viollier et al. 2004; for review, see Wang ical features govern its structure (Fisher et al. 2013). and Rudner 2014). The linear array has been pictured as a In one model, the E. coli chromosome is described as a “bottlebrush” in which interwound loops extrude from a condensed body consisting of a compressed linear array with oriC at the center and the two ends of the array © 2016 Gaal et al. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publi- cation date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). After Corresponding author: [email protected] six months, it is available under a Creative Commons License (At- Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.290312. tribution-NonCommercial 4.0 International), as described at http:// 116. creativecommons.org/licenses/by-nc/4.0/. 2272 GENES & DEVELOPMENT 30:2272–2285 Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/16; www.genesdev.org Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press A bacterial nucleolus central nucleoid scaffold (Le et al. 2013; Wang and Rudner Lewis et al. 2000; Cabrera and Jin 2003; Endesfelder 2014). The ter macrodomain is organized by the MatP and et al. 2013; Jin et al. 2013). Fluorescence-labeled “tran- YfbV proteins (Thiel et al. 2012), but the identities of the scription foci” were observed in fast-growing strains short- and long-range interactions that might organize encoding fusions of GFP to RNAP, correlating with the other parts of the chromosome remain unclear. DNA- high numbers of RNAP molecules expected to be en- binding proteins such as SeqA, SlmA, MukB, and H-NS gaged in transcribing rRNA under these conditions. have been proposed to be important for nucleoid organiza- Consistent with the idea that at least some of these fluo- tion by contributing to the interactions between different rescent foci represented rRNA operons, their intensities loci (Wang and Rudner 2014; Dame Tark-Dame 2016). declined in starved or slowly growing cells. Superresolu- Our interest in E. coli chromosome structure emerged tion imaging showed that RNAPs formed clusters that from our long-term focus on the mechanisms responsible occupied specific regions of the nucleoid under the for ribosome synthesis and its control (Paul et al. 2004). conditions examined; i.e., at fast growth rates when there rRNA synthesis rates are coordinated with the cell’s are large numbers of RNAPs actively transcribing rRNA translational capacity following nutritional shifts such operons (Bratton et al. 2011; Bakshi et al. 2013; Endes- as amino acid starvation. The primary signal molecules felder et al. 2013; Stracy et al. 2015). However, such stud- responsible for adjusting ribosome synthesis rates to ies directly addressed only the locations of RNAP and changing nutritional conditions are ppGpp, an “alar- not the positions of the different rRNA operons. Since mone” whose synthesis is induced by uncharged transfer detection depended on the presence of high numbers of RNAs (tRNAs) in the ribosomal A site (Paul et al. 2004; RNAPs, no information was obtained about the positions Potrykus and Cashel 2008; Ross et al. 2016), and the con- of the rDNA at low growth rates when rRNA transcrip- centration of the initial NTP responsible for forming the tion was low. rRNA transcript (Murray et al. 2003). In contrast to previous studies, we took a direct ap- When cells grow rapidly in rich medium, the majority of proach to address whether rRNA operons are in close the cell’s RNA polymerase (RNAP) is engaged in tran- proximity in space. Using recombineering and counterse- scribing rRNA in order to produce the large number of lection approaches, we inserted sites for different fluores- ribosomes needed to meet the cell’s translational require- cent DNA-binding proteins adjacent to the different ments. Conversely, when cells grow slowly, there is much rRNA operons as well as many other genetic loci. We less rRNA transcription in order to shift the cell’s utiliza- then compared the relative positions of rRNA operons tion of nutritional resources to other priorities (Paul et al. and other genes pairwise in live cells. 2004). The combined effects on rRNA promoters of We show here that most of the rRNA operons are in various regulators—including ppGpp, NTPs, Fis (a nucle- close proximity in space. The physical separation between oid-associated protein that activates rrn P1 promoters), six of the seven rRNA operons (all except rrnC) is in the and other factors—account for the correlation between range of ∼80 to ∼130 nm independent of the genetic dis- growth rate and ribosome synthesis rates, and these fac- tance between them (in kilobases). Our data suggest that tors can compensate for each other in mutants lacking in- E. coli rRNA operons form a structure reminiscent of a eu- dividual regulators (Paul et al. 2004). karyotic nucleolus. The promoter region is necessary A complete understanding of the control of ribosome and sufficient for this “colocalization” of rRNA operons, synthesis depends on identification of not only the cis-act- but, surprisingly, the formation and persistence of the nu- ing sites and the trans-acting factors responsible for regu- cleolus-like structure do not depend on formation of an lation but also the cellular locations of these events in open transcription initiation complex (RPO) or active space and time. In theory, changes in the spatial locations transcription. We speculate that this structure facilitates or organization of the rRNA operons could accompany or ribosome assembly, as has been proposed in eukaryotes, even contribute to the changes in rRNA synthesis rates and that it also contributes to folding of the bacterial that result from changes in nutritional and environmental chromosome.
Load more

Recommended publications
  • 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.
    [Show full text]
  • Chapter 4 – Cell Structure
    Chapter 4 | Cell Structure 107 4 | CELL STRUCTURE Figure 4.1 (a) Nasal sinus cells (viewed with a light microscope), (b) onion cells (viewed with a light microscope), and (c) Vibrio tasmaniensis bacterial cells (seen through a scanning electron microscope) are from very different organisms, yet all share certain basic cell structure characteristics. (credit a: modification of work by Ed Uthman, MD; credit b: modification of work by Umberto Salvagnin; credit c: modification of work by Anthony D'Onofrio, William H. Fowle, Eric J. Stewart, and Kim Lewis of the Lewis Lab at Northeastern University; scale-bar data from Matt Russell) Chapter Outline 4.1: Studying Cells 4.2: Prokaryotic Cells 4.3: Eukaryotic Cells 4.4: The Endomembrane System and Proteins 4.5: The Cytoskeleton 4.6: Connections between Cells and Cellular Activities Introduction Close your eyes and picture a brick wall. What is the wall's basic building block? It is a single brick. Like a brick wall, cells are the building blocks that make up your body. Your body has many kinds of cells, each specialized for a specific purpose. Just as we use a variety of materials to build a home, the human body is constructed from many cell types. For example, epithelial cells protect the body's surface and cover the organs and body cavities within. Bone cells help to support and protect the body. Immune system cells fight invading bacteria. Additionally, blood and blood cells carry nutrients and oxygen throughout the body while removing carbon dioxide. Each of these cell types plays a vital role during the body's growth, development, and day-to-day maintenance.
    [Show full text]
  • 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].
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Self-Assembly of Multi-Component Mitochondrial Nucleoids Via Phase Separa
    bioRxiv preprint doi: https://doi.org/10.1101/822858; this version posted November 12, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. Self-assembly of multi-component mitochondrial nucleoids via phase separa- tion Marina Feric1,2, Tyler G. Demarest3, Jane Tian3, Deborah L. Croteau3, Vilhelm A. Bohr3, and Tom Misteli1,* 1National Cancer Institute, NIH, Bethesda, MD, USA. 2National Institute of General Medical Sciences, NIH, Bethesda, MD, USA. 3National Institute on Aging, NIH, Baltimore, MD, USA. *Correspondence to: [email protected] Abstract Mitochondria contain an autonomous and spatially segregated genome. The organizational unit of mito- chondrial genomes is the nucleoid which consists of mitochondrial DNA (mtDNA) and associated archi- tectural proteins. The physical properties and mechanisms of assembly of mitochondrial nucleoids remain largely unclear. Here, we show that mitochondrial nucleoids form by phase separation. Mitochondrial nu- cleoids exhibit morphological features, coarsening behavior, and dynamics of phase-separated structures in vitro and in vivo. The major mtDNA-binding protein TFAM spontaneously phase separates in vitro into viscoelastic droplets with slow internal dynamics, and the combination of TFAM and mtDNA is suf- ficient to promote the in vitro formation of multiphase structures with gel-like properties, which recapitu- late the in vivo behavior of mitochondrial nucleoids in live human cells. Enlarged phase-separated mito- chondrial nucleoids are present in the premature aging disease Hutchinson-Gilford Progeria Syndrome (HGPS) and altered mitochondrial nucleoid structure is accompanied by mitochondrial dysfunction.
    [Show full text]
  • The Mitochondrial Nucleoid: Integrating Mitochondrial DNA Into Cellular Homeostasis
    Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press The Mitochondrial Nucleoid: Integrating Mitochondrial DNA into Cellular Homeostasis Robert Gilkerson1,2, Liliana Bravo1, Iraselia Garcia1, Norma Gaytan1, Alan Herrera1, Alicia Maldonado2, and Brandi Quintanilla1 1Department of Biology, University of Texas-Pan American, Edinburg, Texas 78539-2999 2Department of Clinical Laboratory Sciences, University of Texas-Pan American, Edinburg, Texas 78539-2999 Correspondence: [email protected] The packaging of mitochondrial DNA (mtDNA) into DNA-protein assemblies called nucle- oids provides an efficient segregating unit of mtDNA, coordinating mtDNA’s involvement in cellular metabolism. From the early discovery of mtDNA as “extranuclear” genetic material, its organization into nucleoids and integration into both the mitochondrial organellar network and the cell at large via a variety of signal transduction pathways, mtDNA is a crucial component of the cell’s homeostatic network. The mitochondrial nucleoid is com- posed of a set of DNA-binding core proteins involved in mtDNA maintenance and transcrip- tion, and a range of peripheral factors, which are components of signaling pathways controlling mitochondrial biogenesis, metabolism, apoptosis, and retrograde mitochon- dria-to-nucleus signaling. The molecular interactions of nucleoid components with the organellar network and cellular signaling pathways provide exciting clues to the dynamic integration of mtDNA into cellular metabolic homeostasis. ORIGINS: “EXTRANUCLEAR DNA” AND later confirmed by the similarity of mtDNA to BIOENERGETICS bacterial, rather than human nuclear, DNA. This “extranuclear” DNA is in fact essential for istorically, it has been clear that mitochon- mitochondrial ATP production (DiMauro and Hdria play by theirown rules.
    [Show full text]
  • A Bacteriophage Tubulin Harnesses Dynamic Instability to Center DNA In
    RESEARCH ARTICLE elifesciences.org A bacteriophage tubulin harnesses dynamic instability to center DNA in infected cells Marcella L Erb1†, James A Kraemer2†, Joanna K C Coker1, Vorrapon Chaikeeratisak1, Poochit Nonejuie1, David A Agard2*, Joe Pogliano1* 1Division of Biological Sciences, University of California, San Diego, La Jolla, United States; 2Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States Abstract Dynamic instability, polarity, and spatiotemporal organization are hallmarks of the microtubule cytoskeleton that allow formation of complex structures such as the eukaryotic spindle. No similar structure has been identified in prokaryotes. The bacteriophage-encoded tubulin PhuZ is required to position DNA at mid-cell, without which infectivity is compromised. Here, we show that PhuZ filaments, like microtubules, stochastically switch from growing in a distinctly polar manner to catastrophic depolymerization (dynamic instability) both in vitro and in vivo. One end of each PhuZ filament is stably anchored near the cell pole to form a spindle-like array that orients the growing ends toward the phage nucleoid so as to position it near mid-cell. Our results demonstrate how a bacteriophage can harness the properties of a tubulin-like cytoskeleton for efficient propagation. This represents the first identification of a prokaryotic tubulin with the dynamic instability of microtubules and the ability to form a simplified bipolar spindle. DOI: 10.7554/eLife.03197.001 *For correspondence: agard@ msg.ucsf.edu (DAA); jpogliano@ ucsd.edu (JP) †These authors contributed Introduction equally to this work Tubulins are universally conserved GTPases that polymerize in a head to tail fashion to form filaments.
    [Show full text]
  • Prokaryotic and Eukaryotic Cells
    Prokaryotic and Eukaryotic Cells Inquire: Prokaryotic vs. Eukaryotic Cells Overview Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus; 2) numerous ​ ​ membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, ​ ​ mitochondria, and others; and 3) several, rod-shaped chromosomes. Because a membrane surrounds a eukaryotic cell’s nucleus, it has a “true nucleus.” The word “organelle” means “little organ,” and as we already mentioned, organelles have specialized cellular functions, just as your body's organs have specialized functions. At this point, it should be clear that eukaryotic cells have a more complex structure than prokaryotic cells. Organelles allow different functions to be compartmentalized in different areas of the cell. Big Question: What are the functions of the major cell structures? ​ ​ Watch: Comparing Prokaryotic and Eukaryotic Cells Have you ever heard the phrase “form follows function?” It’s a philosophy that many industries follow. In architecture, this means that buildings should be constructed to support the activities that will be carried out inside them. For example, a skyscraper should include several elevator banks. A hospital should have its emergency room easily accessible. Our natural world also uses the principle of form following function, especially in cell biology. This use will become clear as we explore prokaryotic and eukaryotic cells. All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like cytosol within the Biology Module 2 - Prokaryotic and Eukaryotic Cells Copyright TEL Library 2018 Page 1 cell in which there are other cellular components; 3) DNA, the cell's genetic material; and 4) ribosomes, which synthesize proteins.
    [Show full text]