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.