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					               Chapter 16



     Prokaryotic cell biology
                    By
Jeff Errington, Matthew Chapman, Scott J.
       Hultgren, & Michael Caparon
         16.1 Introduction

• The relative simplicity of the
  prokaryotic cell architecture
  compared with eukaryotic cells
  belies an economical but highly
  sophisticated organization.
                                 16.1
                                 Introduction

• A few prokaryotic species are well
  described in terms of cell biology.
  – These represent only a tiny sample of
    the enormous diversity represented by
    the group as a whole.


• Many central features of prokaryotic
  cell organization are well conserved.
                                         16.1
                                         Introduction

• Diversity and adaptability have been
  facilitated by a wide range of optional
  structures and processes.
  – These provide some prokaryotes with the
    ability to thrive in specialized and sometimes
    harsh environments.


• Prokaryotic genomes are highly flexible.

• A number of mechanisms enable
  prokaryotes to adapt and evolve rapidly.
16.2 Molecular phylogeny techniques
  are used to understand microbial
              evolution
  • Only a fraction of the prokaryotic
    species on Earth has been analyzed.
16.2 Molecular phylogeny techniques are used to understand
microbial evolution


   • Unique taxonomic techniques have
     been developed for classifying
     prokaryotes.

   • Ribosomal RNA (rRNA) comparison
     has been used to build a three-
     domain tree of life that consists of:
       – Bacteria
       – Archaea
       – Eukarya
16.3 Prokaryotic lifestyles are diverse

  • The inability to culture many
    prokaryotic organisms in the
    laboratory has hindered our
    knowledge about the true diversity
    of prokaryotic lifestyles.
                            16.3 Prokaryotic lifestyles are
                            diverse

• DNA sampling has been used to better
  gauge the diversity of microbial life in
  different ecological niches.

• Prokaryotic species can be characterized
  by their ability to survive and replicate in
  environments that vary widely in:
  –   temperature
  –   pH
  –   osmotic pressure
  –   oxygen availability
16.4 Archaea are prokaryotes with
  similarities to eukaryotic cells
 • Archaea tend to:
   – be adapted to life in extreme
     environments
   – utilize “unusual” energy sources


 • Archaea:
   – have unique cell envelope components
   – lack peptidoglycan cell walls
 16.4 Archaea are prokaryotes with similarities to
 eukaryotic cells

• Archaea resemble bacteria in:
  – their central metabolic processes
  – certain structures, such as flagella


• Archaea resemble eukaryotes in terms of:
  – DNA replication
  – Transcription
  – Translation


• However, gene regulation involves many
  Bacteria-like regulatory proteins
 16.5 Most prokaryotes produce a
polysaccharide-rich layer called the
              capsule
 • The outer surface of many prokaryotes
   consists of a polysaccharide-rich layer
   called the capsule or slime layer.

 • The proposed functions of the capsule or
   slime layer are:
   – to protect bacteria from desiccation
   – to bind to host cell receptors during
     colonization
   – to help bacteria evade the host immune
     system
16.5 Most prokaryotes produce a polysaccharide-rich layer
called the capsule


  • E. coli capsule formation occurs by
    one of at least four different
    pathways.

  • In addition to, or in place of the
    capsule, many prokaryotes have an
    S-layer.
     – This is an outer proteinaceous coat
       with crystalline properties.
16.6 The bacterial cell wall contains a
      crosslinked meshwork of
           peptidoglycan
  • Most bacteria have peptidoglycan:
    – a tough external cell wall made of a polymeric
      meshwork of glycan strands crosslinked with
      short peptides.


  • The disaccharide pentapeptide precursors
    of peptidoglycan are:
    – synthesized in the cytoplasm
    – Exported
    – assembled outside the cytoplasmic membrane
16.6 The bacterial cell wall contains a crosslinked meshwork of
peptidoglycan


    • One model for cell wall synthesis is
      that a multiprotein complex carries
      out insertion of new wall material
      following a “make-before-break”
      strategy.

    • Many autolytic enzymes remodel,
      modify, and repair the cell wall.
16.6 The bacterial cell wall contains a crosslinked meshwork of
peptidoglycan


    • For some bacteria, the
      peptidoglycan cell wall is important
      for maintaining cell shape.

    • A bacterial actin homolog, MreB,
      forms helical filaments in the cell
      cytoplasm.
       – They direct the shape of the cell
         through control of peptidoglycan
         synthesis.
  16.7 The cell envelope of Gram-
positive bacteria has unique features
  • Gram-positive bacteria have a thick
    cell wall containing multiple layers
    of peptidoglycan.

  • Teichoic acids are an essential part
    of the Grampositive cell wall.
    – Their precise function is poorly
      understood.
16.7 The cell envelope of Gram-positive bacteria has
unique features


 • Many Gram-positive cell surface
   proteins are covalently attached to:
    – membrane lipids or
    – peptidoglycan


 • Mycobacteria have specialized lipid-
   rich cell envelope components.
16.8 Gram-negative bacteria have an
 outer membrane and a periplasmic
             space
  • The periplasmic space is found
    between the cytoplasmic and outer
    membranes in Gram-negative
    bacteria.
16.8 Gram-negative bacteria have an outer membrane and a
periplasmic space


    • Proteins destined for secretion
      across the outer membrane often
      interact with molecular chaperones
      in the periplasmic space.

    • The outer membrane is a lipid
      bilayer that prevents the free
      dispersal of most molecules.
16.8 Gram-negative bacteria have an outer membrane and a
periplasmic space


    • Lipopolysaccharide is a component
      of the outer leaflet of the outer
      membrane.

    • During infection by Gram-negative
      bacteria, lipopolysaccharide
      activates inflammatory responses.
16.9 The cytoplasmic membrane is a
   selective barrier for secretion
 • Molecules can pass the cytoplasmic
   membrane by:
   – passive diffusion
   – active translocation
16.9 The cytoplasmic membrane is a selective barrier
for secretion

• Specialized transmembrane
  transport proteins mediate the
  movement of most solutes across
  membranes.

• The cytoplasmic membrane
  maintains a proton motive force
  between the cytoplasm and the
  extracellular milieu.
16.10 Prokaryotes have several
      secretion pathways
• Gram-negative and Gram-positive
  species use the Sec and Tat
  pathways for transporting proteins
  across the cytoplasmic membrane.
          16.10 Prokaryotes have several secretion
          pathways

• Gram-negative bacteria also
  transport proteins across the outer
  membrane.

• Pathogens have specialized
  secretion systems for secreting
  virulence factors.
16.11 Pili and flagella are appendages
     on the cell surface of most
             prokaryotes
  • Pili are extracellular proteinaceous
    structures that mediate many
    diverse functions, including:
    – DNA exchange
    – adhesion
    – biofilm formation by prokaryotes
16.11 Pili and flagella are appendages on the cell surface of
most prokaryotes


   • Many adhesive pili are assembled by
     the chaperone/usher pathway, which
     features:
      – an outer membrane
      – usher proteins that form a pore through
        which subunits are secreted
      – a periplasmic chaperone that:
          • helps to fold pilus subunits
          • guides pilus subunits to the usher
16.11 Pili and flagella are appendages on the cell surface of
most prokaryotes


   • Flagella are extracellular apparati
     that are propellers for motility.

   • Prokaryotic flagella consist of
     multiple segments.
      – Each is formed by a unique assembly of
        protein subunits.
16.12 Prokaryotic genomes contain
  chromosomes and mobile DNA
            elements
 • Most prokaryotes have a single circular
   chromosome.

 • Genetic flexibility and adaptability is
   enhanced by:
   – transmissible plasmids
   – bacteriophages

 • Transposons and other mobile elements
   promote the rapid evolution of
   prokaryotic genomes.
16.13 The bacterial nucleoid and
 cytoplasm are highly ordered
• The bacterial nucleoid appears as a
  diffuse mass of DNA but is highly
  organized.
  – Genes have nonrandom positions in the
    cell.


• Bacteria have no nucleosomes.
  – A variety of abundant nucleoid-
    associated proteins may help to
    organize the DNA.
  16.13 The bacterial nucleoid and cytoplasm are
  highly ordered

• In bacteria, transcription takes place
  within the nucleoid mass.

• Translation takes place within the
  peripheral zone.
  – Analogous to the nucleus and
    cytoplasm of eukaryotic cells

• RNA polymerase may make an
  important contribution to nucleoid
  organization.
 16.14 Bacterial chromosomes are
replicated in specialized replication
              factories
 • Initiation of DNA replication is a key
   control point in the bacterial cell
   cycle.

 • Replication takes place
   bidirectionally from a fixed site
   called oriC.
16.14 Bacterial chromosomes are replicated in specialized
replication factories

    • Replication is organized in
      specialized “factories.”

    • Replication restart proteins facilitate
      the progress of forks from origin to
      terminus.

    • Circular chromosomes usually have
      a termination trap.
       – This ensures that replication forks
         converge in the replication terminus
         region.
16.14 Bacterial chromosomes are replicated in specialized
replication factories


    • Circular chromosomes require special
      mechanisms to coordinate termination
      with:
        –   decatenation
        –   dimer resolution
        –   segregation
        –   cell division


    • The SpoIIIE (FtsK) protein completes the
      chromosome segregation process by
      transporting any trapped segments of
      DNA out of the closing division septum.
   16.15 Prokaryotic chromosome
segregation occurs in the absence of a
           mitotic spindle
  • Prokaryotic cells have no mitotic
    spindle, but they segregate their
    chromosomes accurately.

  • Measurements of oriC positions on
    the chromosome show that they are
    actively separated toward opposite
    poles of the cell early in the DNA
    replication cycle.
16.15 Prokaryotic chromosome segregation occurs in the absence of a
mitotic spindle


    • The mechanisms of chromosome
      segregation are poorly understood.
       – Probably because they are partially
         redundant


    • The ParA-ParB system is probably
      involved in chromosome segregation
      in many bacteria and low-copy-
      number plasmids.
 16.16 Prokaryotic cell division
involves formation of a complex
        cytokinetic ring
• At the last stage of cell division, the cell
  envelope undergoes either:
  – constriction and scission, or
  – septum synthesis followed by autolysis
…to form two separate cells.

• A tubulin homolog, FtsZ, orchestrates the
  division process in bacteria, forming a
  ring structure at the division site.
16.16 Prokaryotic cell division involves formation of a complex
cytokinetic ring


  • A set of about 8 other essential
    division proteins assemble at the
    division site with FtsZ.

  • The cell division site is determined
    by two negative regulatory systems:
      – nucleoid occlusion
      – the Min system
16.17 Prokaryotes respond to stress
with complex developmental changes
  • Prokaryotes respond to stress, such
    as starvation, with a wide range of
    adaptive changes.
16.17 Prokaryotes respond to stress with complex
developmental changes

  • The simplest adaptative responses
    to stress involve:
     – changes in gene expression and
       metabolism
     – a general slowing of the cell cycle,
       preparing the cell for a period of
       starvation

  • In some cases, starvation induces
    formation of highly differentiated
    specialized cell types.
     – For example, the endospores of
       Bacillus subtilis.
16.17 Prokaryotes respond to stress with complex
developmental changes

  • During starvation, mycelial
    organisms such as actinomycetes
    have complex colony morphology
    and produce:
     – aerial hyphae
     – spores
     – secondary metabolites

  • Myxococcus xanthus exemplifies
    multicellular cooperation and
    development of a bacterium.
16.18 Some prokaryotic life cycles
 include obligatory developmental
              changes
 • Many bacteria have been studied as
   simple and tractable examples of
   cellular development and
   differentiation.

 • Caulobacter crescentus is an
   example of an organism that
   produces specialized cell types at
   every cell division.
 16.19 Some prokaryotes and
eukaryotes have endosymbiotic
        relationships
• Mitochondria and chloroplasts arose
  by the integration of free-living
  prokaryotes into the cytoplasm of
  eukaryotic cells.
  – There, they became permanent
    symbiotic residents.
16.19 Some prokaryotes and eukaryotes have endosymbiotic
relationships


   • Rhizobia species form nodules on
     legumes:
      – So that elemental nitrogen can be
        converted into the biologically active
        form of ammonia.


   • The development and survival of pea
     aphids depends on an endosymbiotic
     event with Buchnera bacteria.
16.20 Prokaryotes can colonize and
 cause disease in higher organisms
 • Although many microbes make their
   homes in or on the human body, only a
   small fraction cause harm to us.

 • Pathogens are often able to:
   – colonize
   – replicate
   – survive within host tissues

 • Many pathogens produce toxic substances
   to facilitate host cell damage.
16.21 Biofilms are highly organized
     communities of microbes
 • It has been estimated that most of
   the Earth’s prokaryotes live in
   organized communities called
   biofilms.
      16.21 Biofilms are highly organized communities of
      microbes

• Biofilm formation involves several
  steps including:
  –   surface binding
  –   growth and division
  –   polysaccharide production
  –   biofilm maturation
  –   dispersal

• Organisms within a biofilm
  communicate by quorum sensing
  systems.

				
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