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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.

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Chapter 16 l.jpg

Chapter 16

Prokaryotic cell biology

By

Jeff Errington, Matthew Chapman, Scott J. Hultgren, & Michael Caparon


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16.1 Introduction

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


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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.


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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.


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16.2 Molecular phylogeny techniques are used to understand microbial evolution

  • Only a fraction of the prokaryotic species on Earth has been analyzed.


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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


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16.3 Prokaryotic lifestyles are diverse microbial evolution

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


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16.3 Prokaryotic lifestyles are diverse microbial evolution

  • 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


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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


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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


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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


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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.


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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


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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.


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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.


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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.


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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.


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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.


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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.


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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.


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16.9 The cytoplasmic membrane is a selective barrier for secretion

  • Molecules can pass the cytoplasmic membrane by:

    • passive diffusion

    • active translocation


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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.


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16.10 Prokaryotes have several secretion pathways secretion

  • Gram-negative and Gram-positive species use the Sec and Tat pathways for transporting proteins across the cytoplasmic membrane.


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16.10 Prokaryotes have several secretion pathways secretion

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

  • Pathogens have specialized secretion systems for secreting virulence factors.


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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


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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


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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.


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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.


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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.


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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.


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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.


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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.


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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.


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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.


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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.


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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.


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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


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16.17 Prokaryotes respond to stress with complex developmental changes

  • Prokaryotes respond to stress, such as starvation, with a wide range of adaptive changes.


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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.


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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.


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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.


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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.


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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.


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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.


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16.21 Biofilms are highly organized communities of microbes organisms

  • It has been estimated that most of the Earth’s prokaryotes live in organized communities called biofilms.


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16.21 Biofilms are highly organized communities of microbes organisms

  • 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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