Chapter 16

Prokaryotic cell biologyBy

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.

• 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.

16.1 Introduction

16.2 Molecular phylogeny techniques are used to understand

microbial evolution• Only a fraction of the prokaryotic

species on Earth has been analyzed.

• 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

16.2 Molecular phylogeny techniques are used to understand microbial evolution

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.

• 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

16.3 Prokaryotic lifestyles are diverse

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

• 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

16.4 Archaea are prokaryotes with similarities to eukaryotic cells

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

• 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.

16.5 Most prokaryotes produce a polysaccharide-rich layer called the capsule

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

• 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.

16.6 The bacterial cell wall contains a crosslinked meshwork of peptidoglycan

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.

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

• Mycobacteria have specialized lipid-rich cell envelope components.

16.7 The cell envelope of Gram-positive bacteria has unique features

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.

• 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.

16.8 Gram-negative bacteria have an outer membrane and a periplasmic space

16.9 The cytoplasmic membrane is a selective barrier for secretion

• Molecules can pass the cytoplasmic membrane by:– passive diffusion– active translocation

• 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.

16.9 The cytoplasmic membrane is a selective barrier for secretion

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.

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

• Pathogens have specialized secretion systems for secreting virulence factors.

16.10 Prokaryotes have several secretion pathways

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

• 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.

16.11 Pili and flagella are appendages on the cell surface of most prokaryotes

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.

• 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.

16.13 The bacterial nucleoid and cytoplasm are highly ordered

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.

• 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.

16.14 Bacterial chromosomes are replicated in specialized replication factories

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.

• 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.

16.15 Prokaryotic chromosome segregation occurs in the absence of a mitotic spindle

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.

• 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

16.16 Prokaryotic cell division involves formation of a complex cytokinetic ring

16.17 Prokaryotes respond to stress with complex developmental

changes• Prokaryotes respond to stress,

such as starvation, with a wide range of adaptive 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.

16.17 Prokaryotes respond to stress with complex developmental changes

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.

• 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.

16.19 Some prokaryotes and eukaryotes have endosymbiotic relationships

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.

• 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.

16.21 Biofilms are highly organized communities of microbes