1. Prokaryotic Cell Biology

2. Figure 20.1: General structure of a prokaryotic cell.
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, but these represent only a tiny sample of the enormous diversity represented by the group as a whole.
Figure 20.1: General structure of a prokaryotic cell.

3. Figure 20.2: Bacterial cell envelopes.
Introduction
Figure 20.2: Bacterial cell envelopes.

4. Introduction
Many central features of prokaryotic cell organization are well conserved throughout cellular life.
Diversity and adaptability have been facilitated by a wide range of optional structures and processes that provide some prokaryotes with the ability to thrive in specialized and sometimes harsh environments.
Bacteria colonize nearly every environmental niche on Earth, including our own bodies. On average bacteria in our bodies outnumber our own cells 10–100:1.
Prokaryotic genomes are highly flexible and a number of mechanisms enable prokaryotes to adapt and evolve rapidly.

5. 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, and eukarya.

6. Figure 20.4: Classification of organisms based on molecular phylogeny.

7. 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, and oxygen availability.

8. Archaea are prokaryotes with similarities to eukaryotic cells
Archaea tend to be adapted to life in extreme environments and to utilize “unusual” energy sources.
Archaea have unique cell envelope components and lack peptidoglycan cell walls.
Archaea resemble bacteria in their central metabolic processes and certain structures, such as flagella.

9. Archaea resemble eukaryotes in terms of DNA replication, transcription, and translation, but gene regulation involves many bacteria-like regulatory proteins.
Figure 20.7: Archaea have features in common with bacteria and eukaryotes.

10. 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, and to help bacteria evade the host immune system.

11. Prokaryotes produce 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, an outer proteinaceous coat with crystalline properties.

12. The bacterial cell wall contains a cross-linked meshwork of peptidoglycan
Most bacteria have peptidoglycan, a tough external cell wall made of a polymeric meshwork of glycan strands cross-linked with short peptides.
The disaccharide pentapeptide precursors of peptidoglycan are synthesized in the cytoplasm, exported, and assembled outside the cytoplasmic membrane.

13. Figure 20.11: Formation of peptidoglycan.
Bacterial cell wall
Figure 20.11: Formation of peptidoglycan.

14. Bacterial cell wall
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.

15. Figure 20.14: Mutations in mreB or mbl after cell shape.
Bacterial cell wall
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 that direct the shape of the cell through control of peptidoglycan synthesis.
Figure 20.14: Mutations in mreB or mbl after cell shape.
Reprinted from Cell, vol. 104, L. J. F. Jones, R. Caballido-López, and J. Errington, Control of cell shape in bacteria..., pp , Copyright (2001) with permission from Elsevier [ Photos courtesy of Jeffrey Errington, Institute for Cell and Molecular Biosciences, Newcastle University.

16. 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 Gram-positive cell wall, but their precise function is poorly understood.
Figure 20.16: Structure of teichoic acids.

17. Figure 20.18: Sortase pathway for anchoring proteins to the cell wall.
Cell envelope
Many Gram-positive cell surface proteins are covalently attached to membrane lipids or to peptidoglycan.
Mycobacteria have specialized lipid-rich cell envelope components.
Figure 20.18: Sortase pathway for anchoring proteins to the cell wall.

18. 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.
Figure 20.21: The cell envelope of Gram-negative bacteria.

19. 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.
Lipopolysaccharide is a component of the outer leaflet of the outer membrane.
During infection by Gram-negative bacteria, lipopolysaccharide activates inflammatory responses.

20. The cytoplasmic membrane is a selective barrier for secretion
Molecules can pass the cytoplasmic membrane by passive diffusion or 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.

21. Prokaryotes have several secretion pathways
Gram-negative and Gram-positive species use the Sec and Tat pathways for transporting proteins across the cytoplasmic membrane.
Figure 20.25: The Sec secretion pathway.

22. Prokaryotes have several secretion pathways
Gram-negative bacteria also transport proteins across the outer membrane
Pathogens have specialized secretion systems for secreting virulence factors.

23. 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, and biofilm formation by prokaryotes.

24. Figure 20.28: The PapD chaperone functions in pilus assembly.
Pili and flagella
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, and a periplasmic chaperone that helps to fold pilus subunits and guides them to the usher.
Figure 20.28: The PapD chaperone functions in pilus assembly.

25. Figure 20.29: Different flagella arrangements in bacteria.
Pili and flagella
Flagella are extracellular apparati that are propellers for motility.
Prokaryotic flagella consist of multiple segments, each of which is formed by a unique assembly of protein subunits.
Figure 20.29: Different flagella arrangements in bacteria.

26. Prokaryotic genomes contain chromosomes and mobile DNA elements
Most prokaryotes have a single circular chromosome.
Genetic flexibility and adaptability is enhanced by transmissible plasmids and by bacteriophages.
Transposons and other mobile elements promote the rapid evolution of prokaryotic genomes.

27. Prokaryotic genomes contain chromosomes and mobile DNA elements
Figure 20.32: Bacterial plasmids and their functions.

28. The bacterial nucleoid and cytoplasm are highly ordered
The bacterial nucleoid appears as a diffuse mass of DNA but is highly organized, and genes have nonrandom positions in the cell.
Bacteria have no nucleosomes, but a variety of abundant nucleoid-associated proteins may help to organize the DNA.
In bacteria, transcription takes place within the nucleoid mass; translation, the peripheral zone—analogous to the nucleus and cytoplasm of eukaryotic cells.
RNA polymerase may make an important contribution to nucleoid organization.

29. 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.”

30. Bacterial chromosomes
Replication restart proteins facilitate the progress of forks from origin to terminus.
Circular chromosomes usually have a termination trap, which ensures that replication forks converge in the replication terminus region.
Figure 20.39: A model for bacterial chromosome replication.

31. Bacterial chromosomes
Circular chromosomes require special mechanisms to coordinate termination with decatenation, dimer resolution, segregation, and cell division.
The SpoIIIE (FtsK) protein completes the chromosome segregation process by transporting any trapped segments of DNA out of the closing division septum.

32. 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.

33. Prokaryotic chromosome segregation
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.

34. Figure 20.41: Prokaryotice cells divide by constriction or septation.
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.
Figure 20.41: Prokaryotice cells divide by constriction or septation.

35. Prokaryotic cell division
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 and the Min system.

36. Prokaryotic cell division
Figure 20.44: MinCD inhibits FtsZ ring formation.

37. 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, and a general slowing of the cell cycle, preparing the cell for a period of starvation.
Figure 20.46: Regulation of the RNA polymerase subunit.

38. Prokaryotes respond to stress with complex developmental changes
In some cases, starvation induces formation of highly differentiated specialized cell types, such as the endospores of B. subtilis.
During starvation, mycelial organisms such as actinomycetes have complex colony morphology and produce aerial hyphae, spores, and secondary metabolites.
Myxococcus xanthus exemplifies multicellular cooperation and development of a bacterium.

39. Prokaryotes respond to stress with complex developmental changes
Figure 20.53: The C-signal initiates sporulation of M. xanthus.

40. 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.

41. Some prokaryotes and eukaryotes have endosymbiotic relationships
Mitochondria and chloroplasts arose by the integration of free-living prokaryotes into the cytoplasm of eukaryotic cells where 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.

42. 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, and survive within host tissues.
Many pathogens produce toxic substances to facilitate host cell damage.

43. 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 and biofilm maturation, and dispersal.
Organisms within a biofilm communicate by quorum-sensing systems.

44. Biofilms are highly organized communities of microbes
Figure 20.58: Steps in biofilm development.