MIC2011 Week 2

membrane lipid bonds: Bacteria vs. Archaea

• bacteria: ester bonds link fatty acids to glycerol

• archaea: ether bonds link isoprenoids to glycerol

• result: archaeal membranes are more stable

membrane structure: monolayer capability

• bacteria: always a lipid bilayer

• archaea: can form a monolayer (two head groups with very long tails spanning the entire width)

• this is a unique feature of Archaea due to ether linkages

peptidoglycan presence

• bacteria: yes. unique to this domain. composed of glycan chains cross-linked by peptides (contains non-standard amino acids)

• archaea: no. they never have peptidoglycan

most common cell wall material

• bacteria: peptidoglycan (thick in Gram-positive, thin in Gram-negative)

• archaea: s-layer (crystalline protein layer) is the most common architecture

alternate cell wall polymer (if not peptidoglycan)

• bacteria: (no alternate polymer; it's either peptidoglycan or no wall like Mycoplasma)

• archaea: pseudopeptidoglycan (or Pseudomurein). looks similar but is chemically distinct from bacterial peptidoglycan

why do Archaea require less reinforcement from the cell wall

• archaea have more stable membrane chemistry (ether linkages, isoprenoid tails, possible monolayers)

• they are inherently more resistant to chemical/thermal destabilization than bacterial ester-linked bilayers

outer membrane presence

• bacteria: present in Gram-negative bacteria only (contains Lipopolysaccharide/LPS)

• archaea: absent. (archaea do not have an outer membrane like Gram-negative bacteria)

gram-positive envelope: antimicrobial vulnerability (advantage for host/medicine)

high susceptibility to cell wall antibiotics.

• target: thick, exposed peptidoglycan layer

• drugs: Penicillins, Cephalosporins (block synthesis), Lysozyme (degrades it)

• result: without outer membrane protection, these drugs easily access their lethal target

gram-positive envelope: disadvantage (for the bacterium)

lack of protective outer membrane.

• consequence: vulnerable to bile salts, digestive enzymes, and desiccation compared to Gram-negatives

• immune evasion: lacks Lipopolysaccharide (LPS) , so must rely entirely on surface proteins or capsule for hiding

gram-negative envelope: major advantage (barrier function)

outer membrane (OM) acts as selective shield

• permeability barrier: Lipopolysaccharide (LPS) outer leaflet blocks large/hydrophobic molecules (bile salts, many antibiotics)

• controlled entry: forces nutrients and drugs through narrow porins, limiting uptake rates

gram-negative envelope: relevance to antimicrobial resistance

intrinsic resistance mechanism

• many antibiotics (Vancomycin, Penicillin G) cannot cross the OM easily

• bacteria can further evolve porin mutations (smaller holes) to exclude drugs

• periplasm: houses enzymes (β-lactamases) that destroy antibiotics before they reach the inner membrane target

gram-negative envelope: critical disadvantage (pathogenesis)

LPS (endotoxin) is toxic to host.

• lipid A portion triggers massive immune overreaction (fever, septic shock) if bacteria are lysed

• disadvantage for the bacterium: makes infection more severe and symptomatic, alerting host defenses early

• relevance: treating Gram-negative infections requires care to avoid massive endotoxin release

mycobacteria envelope: advantage & antimicrobial relevance

waxy mycomembrane (mycolic acid layer)

• advantage: extremely impermeable to chemicals, desiccation, and most standard antibiotics (resistant to Penicillin/Lysozyme)

• disadvantage: slow growth due to restricted nutrient diffusion

• relevance: requires specific, long-course antibiotics (Isoniazid, Ethambutol) that target mycolic acid synthesis

mycoplasma envelope: advantage & antimicrobial relevance

complete lack of cell wall

• advantage: intrinsic resistance to ALL cell wall-active drugs (Penicillins, Cephalosporins, Vancomycin, Lysozyme). no target present

• disadvantage: mechanically fragile; requires specialized environment (host cell interior) or sterols in membrane for rigidity

• relevance: treat with drugs targeting protein synthesis (Tetracyclines) or membranes, never β-lactams

archaeal envelope: antimicrobial relevance

resistance to standard wall drugs

• peptidoglycan is absent. therefore, Lysozyme, Penicillins, and Cephalosporins are INEFFECTIVE

• membrane disruptors (Lipopeptides): may still work if they target membrane integrity, but ether-linked isoprenoid membranes are often more stable/less fluid

capsule: advantages for survival & resistance

1. phage shield: masks cell wall receptors; prevents bacteriophage attachment

2. immune evasion: masks underlying antigens (peptidoglycan) from host antibodies/complement

3. desiccation resistance: retains water for survival on dry hospital surfaces

4. biofilm matrix: aids sticky attachment

capsule: disadvantages (evolutionary trade-off)

1. energetically expensive: huge carbon/nutrient cost to build the polysaccharide layer

2. vaccine target: exposed capsule is the primary antigen for vaccines (S. pneumoniae PCV13)

3. phage therapy exploit: if bacteria lose capsule to resist a phage, they lose virulence and become susceptible to immune clearance (A. baumannii example)

periplasm: advantage vs. disadvantage

• advantage: enzyme trap. retains digestive enzymes and binding proteins close to the cell; site of peptidoglycan synthesis and early antibiotic inactivation

• disadvantage: transport cost. requires complex energy-dependent transport systems to move nutrients across two membranes, potentially limiting uptake rate

which antimicrobials work on Gram-Positive bacteria

• lysozyme (degrades thick peptidoglycan)

• penicillins / cephalosporins (block peptidoglycan synthesis)

• lipopeptides (disrupt cytoplasmic membrane)

• note: vancomycin works well on Gram-positives but cannot cross Gram-negative outer membrane

which antimicrobials work on Gram-Negative bacteria

• some cephalosporins (must be small enough to pass through porins)

• lipopeptides (disrupt inner membrane if they can bypass LPS)

• note: Lysozyme and Penicillin G are generally ineffective unless outer membrane is first damaged/disrupted

Cell Wall: Primary Function

resists osmotic pressure

• prevents cell lysis due to high internal solute concentration driving water influx

• without wall: cell becomes spherical protoplast and lyses

• provides mechanical strength and protection from membrane-destabilizing chemicals

Peptidoglycan (Murein)

• composition: repeating glycan units cross-linked by short peptides (contains non-standard amino acids)

• properties: strong, flexible, porous

• location: unique to Bacteria (not in Archaea or Eukaryotes)

Teichoic Acids: Function

• surface polysaccharides anchored in the thick peptidoglycan or membrane

• functions:

  1. promote attachment to host tissues/surfaces

  2. mediate host interaction

  3. contribute to overall cell wall negative charge

Outer Membrane (OM): Structure & Function

• structure: inner leaflet (phospholipids), outer leaflet (Lipopolysaccharide / LPS)

• function: permeability barrier against bile salts, digestive enzymes, and large antibiotics

• porins: protein channels allowing passive diffusion of small nutrients

LPS (Lipopolysaccharide): Components & Roles

• Lipid A: anchors LPS; acts as endotoxin (toxic to animals)

• core polysaccharide: relatively conserved structure

• O-Antigen: highly variable polysaccharide chain extending outward; key for immune evasion and serotyping

Periplasm: Definition & Function

• definition: gel-like compartment between inner and outer membranes (~15 nm wide)

• function:

  1. prevents extracellular enzymes from diffusing away

  2. site of peptidoglycan synthesis and nutrient digestion

  3. location of binding proteins for transport

S-Layer (Surface Layer)

• structure: crystalline protein layer (most common archaeal wall)

• function:

  1. permeability barrier

  2. maintains cell shape/structure

  3. immune interaction/evasion

• note: always the outermost layer when present

Mycomembrane (Mycolic Acid Layer)

• structure: waxy, lipid-rich outer layer (mycolic acids) external to peptidoglycan

• function: extreme impermeability barrier; protects against drying, chemicals, and many antibiotics

• found in: Mycobacteria (M. tuberculosis)

Capsule: Structure & Key Functions

• structure: thick polysaccharide layer (rarely other polymers); tightly or loosely bound (slime layer)

• functions:

  1. immune evasion: masks underlying antigens from antibodies/phages

  2. desiccation resistance: hydrophilic; retains water

  3. nutrient acquisition: slows diffusion, traps enzymes

  4. biofilm attachment

Capsule: What it is NOT for

• does NOT provide mechanical strength or shape. (that is the cell wall's role)

• loss of capsule does not cause lysis, but often results in loss of virulence

Bacterial Flagellum: Structure & Energy

• function: swimming motility (rotary motor, up to 500 μm/sec)

• structure: long (5-10 μm), hollow filament (flagellin protein), hook, and complex basal body anchor

• energy source: proton motive force (PMF) across cytoplasmic membrane

Archaeal Archaellum: Structure & Energy

• function: swimming motility (convergent evolution; unrelated to flagellum)

• structure: narrower, solid filament (pilin-like proteins), simple membrane anchor (no complex basal body)

• energy source: ATP hydrolysis

Pili (Fimbriae): General Features & Attachment

• structure: thin (2-10 nm), filamentous protein surface appendages

• function 1: attachment. adhesin proteins at tip bind specifically to surfaces/host cells (UPEC binding to bladder epithelium)

Pili: Twitching Motility

• mechanism: "grappling hook." pilus extends → attaches to surface → retracts (ATP-powered) → pulls cell forward

• domain: observed in Bacteria (not yet in Archaea)

Pili: Genetic Exchange

• conjugation: specialized sex pilus joins donor and recipient cells; DNA passes through central channel

• transformation: DNA-binding proteins at pilus tip take up environmental DNA

• domain: observed in Bacteria

Gas Vesicles: Structure & Function

• structure: gas-permeable protein "cages" with hydrophobic inner shell

• function: buoyancy regulation. allows aquatic prokaryotes to float to optimal light/oxygen levels

• advantage: passive inflation; no ongoing energy cost

Endospore: Function & Key Trait

• function: dormant survival structure (not reproduction)

• resistance: extreme heat, drying, radiation, chemicals/antibiotics (due to low water content and multiple protective layers)

• domain: found only in a few genera of Bacteria (Clostridium, Bacillus). not found in Archaea

Surface Structures Unique to Bacteria (vs. Archaea)

• peptidoglycan cell wall

• outer membrane / LPS

• teichoic acids

• endospores

• conjugation pili

• twitching motility

Surface Structures Common or Unique to Archaea

• S-Layer (most common wall type)

• pseudopeptidoglycan (analogous to peptidoglycan, chemically distinct)

• archaellum (solid, ATP-driven)

• capsules are rare; pili are present but conjugation/twitching not observed

what is the nucleoid in prokaryotes

the genetic material + packaging proteins organized into a distinct region visible by microscopy

• no nuclear membrane (unlike eukaryotes)

• ribosomes are excluded from this region

• DNA is many times longer than the cell and must be compacted

How is DNA packaged in Bacteria? (Mechanism & Proteins)

• supercoiling: DNA loops fold back due to enzyme-introduced tension → "bottlebrush" structure

• packaging proteins: NAPs (nucleoid-associated proteins) only. no histones

• NAP actions: bridging, bending, and coating DNA to balance compaction with accessibility

How is DNA packaged in Archaea?

archaea use two strategies (mix of bacterial and eukaryotic features):

1. histones: form nucleosome-like structures (DNA wrapped around histone core)

2. NAPs: nucleoid-associated proteins analogous to bacteria

Describe the prokaryotic cytoplasm environment

• extremely crowded: ~3× higher macromolecule concentration than egg white

• site of: translation (protein synthesis) and metabolic reactions

• simultaneous events: transcription (RNA synthesis at nucleoid edge) and translation (ribosomes outside) occur simultaneously (no nuclear membrane barrier)

Prokaryotic Ribosomes: Appearance & Domain Difference

• appearance: thousands per cell give cytoplasm a "grainy" texture on TEM

• bacteria: bacterial-type ribosome components

• archaea: ribosome components are more similar to eukaryotes than to bacteria

Prokaryotic Cytoskeleton: Presence & Functions

• presence: homologues of actin, tubulin, and intermediate filaments found in both Bacteria and Archaea

• functions:

  1. cell division (FtsZ ring)

  2. segregation of DNA copies to daughter cells

  3. organization of cell wall synthesis (MreB forms curved filaments guiding wall growth)

  4. protein/inclusion localization

Storage Inclusions: Purpose & Why Membrane-Enclosed?

• purpose: store excess nutrients (C, P, S) without altering cytoplasmic osmotic balance

• examples:

  • PHB granules (Carbon/Poly-β-hydroxybutyric acid)

  • volutin granules (Phosphate)

  • sulfur globules (Sulfur)

• why enclosed? prevents osmotic stress and allows accumulation beyond normal solubility limits

Bacterial Microcompartments: Structure & Example

• structure: enzymes bounded by a protein shell (not a lipid membrane)

• function: concentrates metabolites and enzymes to increase reaction efficiency/avoid toxic intermediates

• example: carboxysomes – site of carbon fixation in cyanobacteria and some chemoautotrophs

Gas Vesicles: Structure, Function & Energy Cost

• structure: gas-permeable protein "cages" with hydrophobic inner surface

• function: buoyancy regulation; allows aquatic prokaryotes to float to optimal light/oxygen levels

• inflation: passive (gas diffuses in as protein shell grows; water excluded)

• advantage: no ongoing energy cost (unlike flagella swimming)

Endospores: Definition & Key Features

• what: dormant, highly resistant survival cells (NOT reproductive)

• structure: extremely low water content + multiple protective protein/membrane layers

• resistance: extreme heat, drying, radiation, chemicals/antibiotics

• domain: found ONLY in some Bacteria (Clostridium, Bacillus). never in Archaea

Membrane Lipid Linkage: Ester bonds
→ Bacteria or Archaea?

bacteria

• (ester bonds link fatty acids to glycerol)

• archaea use ether bonds

Membrane Lipid Linkage: Ether bonds
→ Bacteria or Archaea?

archaea

• (ether bonds link isoprenoids to glycerol)

• Bacteria use Ester bonds.

Membrane Structure: Can form a monolayer
→ Bacteria or Archaea?

archaea

• some archaea have tetraether lipids spanning the entire membrane (two head groups, very long tails)

• bacteria always have a bilayer

Cell Wall Contains Peptidoglycan
→ Bacteria or Archaea?

bacteria (unique to this domain)

• Archaea have Pseudopeptidoglycan or S-layer, never true peptidoglycan

Cell Wall: Most common type is an S-layer (crystalline protein)
→ Bacteria or Archaea?

Archaea

• S-layer is the most common archaeal cell wall architecture

• bacteria primarily use peptidoglycan; S-layer is present in some but not the default

Outer Membrane containing Lipopolysaccharide (LPS)
→ Bacteria or Archaea?

Bacteria (specifically Gram-negative bacteria)

• Archaea do not have an outer membrane with LPS

Swimming Structure: Hollow filament made of flagellin, powered by Proton Motive Force (PMF)
→ Bacteria or Archaea?

Bacterial Flagellum

• hollow, flagellin subunits, complex basal body + hook, driven by PMF

Swimming Structure: Solid filament made of pilin-like proteins, powered by ATP
→ Bacteria or Archaea?

Archaeal Archaellum

• solid, narrower, simple membrane anchor, driven by ATP hydrolysis

• homologous to bacterial Type IV pili

Twitching Motility (grappling hook pili) observed
→ Bacteria or Archaea?

Bacteria

• twitching motility via Type IV pili has been observed in bacteria

• not yet observed in Archaea

Conjugation (DNA transfer via specialized pilus) observed
→ Bacteria or Archaea?

Bacteria

• conjugation pili and DNA transfer observed in bacteria

• not yet observed in Archaea

Capsules (polysaccharide layers) are common
→ Bacteria or Archaea?

Bacteria

• Capsules are common in bacteria, important for virulence and immune evasion

• Capsules are rare in Archaea

DNA Packaging: NAPs only (no histones)
→ Bacteria or Archaea?

Bacteria

• Bacterial DNA is organized by nucleoid-associated proteins (NAPs) only

• Archaea may use histones OR NAPs

DNA Packaging: Histones (eukaryote-like nucleosomes)
→ Bacteria or Archaea?

Archaea

• some archaea wrap DNA around histone proteins, forming nucleosome-like structures

• Bacteria never use histones

Chromosome Shape: Can be linear
→ Bacteria or Archaea?

Bacteria

• most bacteria have circular chromosomes, but linear chromosomes exist in some (Borrelia, Streptomyces).

• all known archaea have circular chromosomes.

Endospores (dormant, highly resistant cells) produced
→ Bacteria or Archaea?

Bacteria only (a few genera like Clostridium, Bacillus)

• no archaea are known to produce endospores

Ribosome Type: More similar to eukaryotes
→ Bacteria or Archaea?

Archaea

• Archaeal ribosome components share more similarity with eukaryotic ribosomes

• Bacterial ribosomes are distinctly "bacterial-type"

You isolate a prokaryote. It has an ether-linked membrane, an S-layer cell wall, and uses histones to package DNA. Identify the domain.

Archaea
Key markers:

• ether-linked membrane

• S-layer (or pseudopeptidoglycan)

• histone-based DNA packaging

You isolate a prokaryote. It has an ester-linked bilayer membrane, peptidoglycan cell wall, and forms heat-resistant endospores. Identify the domain.

Bacteria
key markers:

• ester-linked membrane

• peptidoglycan

• endospore formation (some species)

You observe a motile prokaryote with a hollow filament rotating via PMF and a complex basal body spanning the envelope. Identify the domain.

Bacteria

• this describes a bacterial flagellum (hollow, flagellin, PMF-driven, complex anchor)

You observe a motile prokaryote with a solid, narrow filament driven by ATP and a simple membrane anchor. Identify the domain.

Archaea

• this describes an archaellum (solid, pilin-like, ATP-driven, simple anchor)