Week 2 - Bacteria

Magnetostatic bacteria

Use magnets formed from iron in the environment to navigate underwater, using Earth’s magnetic fields. An example of prokaryotes with membrane-bound organelles (magnetosomes)

Spherical bacteria

Coccus/cocci

Rod-shaped bacteria

Bacillus/bacilli

Comma-shaped bacteria

Vibrio/vibrios

Spiral bacteria

Spirillum/spirilla

Pleiomorphic bacteria

Varied shapes of bacteria

Hyphae

Branching filaments of cells

Mycelia

Tufts of hyphae

Trichomes

Smooth, unbranched chains of bacteria

Size of prokaryotes vs eukaryotes

Bacteria are typically 0.5 to 5 um in length, while eukaryal cells are bigger. Bacteria have extensive size variation

3 multicellular arrangements of bacteria

• Diplo: pairs of cells

• Strepto: chains of cells

• Staphylo: clusters

Nucleoid (composition + function)

• Composed of DNA, RNA, and protein, in bacterial cytoplasm

• Stores genetic info, coated with proteins and RNA being synthesized

Chromosome-packaging proteins (composition + function)

• Composed of protein, in bacterial cytoplasm

• Protects and compacts DNA

Enzymes involved in DNA and RNA synthesis (composition + function)

• Composed of proteins, in bacterial cytoplasm

• Transcription

Regulatory factors (composition + function)

• Composed of proteins and RNA, in bacterial cytoplasm

• Control replication, transcription, and translation

Ribosomes (composition + function)

• Composed of RNA and proteins, in bacterial cytoplasm

• Translation

Plasmid (composition + function)

• Composed of DNA, in bacterial cytoplasm

• Encode non-chromosomal genes, extra pieces of DNA

Enzymes that break down substrates (composition + function)

• Composed of proteins, in bacterial cytoplasm

• Produce energy, provide anabolic precursors

Inclusion bodies (composition + function)

• Composed of various polymers, in bacterial cytoplasm

• Store carbon, phosphate, nitrogen, and sulfur

Gas vesicles (composition + function)

• Composed of proteins, in bacterial cytoplasm

• Maintain buoyancy, letting the cell float up or down

Magnetosomes (composition + function)

• Composed of proteins, lipids, and iron, in bacterial cytoplasm

• Orient the cell during movement (navigation), form long chains organized by protein filaments

Cytoskeletal structures (composition + function)

• Composed of protein, in the cytoplasm

• Guides cell wall synthesis and division, maintains cell shape

Polyhydroxybutyrate granules

Type of inclusion body for carbon storage. Can compose over 50% of a cell’s dry weight

Sulfur globules

Type of inclusion body for sulfur storage

Carboxysomes

Location of carbon fixation reactions (photosynthesis), in bacterial cytoplasm

Method that bacteria store large chromosomes

Supercoiling DNA in the nucleoid

FtsZ

• Cytoskeleton, tubulin-related protein

• Forms the Z-ring which contracts to pinch the cell in two as FtsZ breaks down

MreB

• Cytoskeletal, actin-like protein

• Provides structure in non-spherical bacteria by guiding cell wall synthesis and forming long helical filaments under the membrane

ParM

• Cytoskeletal protein

• Directs plasmid movement, ensuring plasmid segregation

MamK

• Cytoskeletal, actin-like protein

• Required for magnetosome function, which will disappear if MamK is mutated

FtsZ is to microtubules as MreB is to…

Microfilaments

Plasma membrane (PM)

• Composed of a phospholipid bilayer with embedded proteins

• Separates the interior of the cell from the environment

Hopanoids

Sterol-like molecules in the PM, help with stability across temperature ranges

Hopanoids vs cholesterol

Hopanoids are abundant in prokaryotes while cholesterol is abundant in eukaryotes

Diffusion

Small gases like O2 and CO2 can diffuse across the cell membrane readily

Osmosis + related protein

The movement of water across a plasma membrane from low to high solute concentration, often through aquaporins

How do bacterial cells withstand pressure from osmosis?

Having a strong cell well to maintain shape

Facilitated diffusion

Using a protein channcel to move particles along a concentration gradient

Active transport

Using ATP/energy to move particles against a concentration gradient

Symport/antiport

Active co-transporters where two substances are either moved in the same direction or opposite directions

ABC transporters (4 steps)

ATP binds to these proteins to transport materials across a membrane

1. Binding protein grabs the solute of interest outside the cell

2. Binding protein delivers the solute to the ABC transporter

3. Transporter changes shape and opens a channel

4. ATP hydrolysis powers the opening/closing cycle

Electron transport chains (ETC)

Embedded in the PM, create energy (proton motive force, PMF)

Protein secretion in the PM (4 steps)

1. Signal peptide marks proteins that the cell needs to secrete

2. SecB binds and keeps the protein unfolded

3. SecA uses ATP to push the protein through the SecYEG membrane channel

4. Once outside the membrane, the signal peptide is cut off, and the protein folds

Bacterial cell wall composition + function

Crosslinked strands of peptidoglycan subunits (NAM and NAG), giving cells their shape and protecting them from osmotic lysis

NAM vs NAG

NAM has a small peptide chain attached, which varies by species (the way they’re crosslinked can also vary)

Why are the amino acids associated with NAM unusual?

They appear in the D form of the molecule (the less common stereoisomer) instead of the L form

Formation of the cell wall (6 steps)

1. NAM is linked to a peptide in the cytoplasm

2. NAM-peptide attaches to bactoprenol in the membrane

3. NAG is added, forming the NAM-NAG unit

4. Bactoprenol flips the NAM-NAG unit across the membrane

5. The unit is added to the growing cell wall and transpeptidase crosslinks the peptides

6. Bactoprenol flips back to pick up the next unit

Lysozyme

Breaks the NAM-NAG B-1,4 glycosidic bond, degrading the cell wall

Lysostaphin

Cuts the glycine-glycine link in the peptidoglycan cross-bridge, causing the cell to round up into a protoplast and degrade the cell wall.

B-lactam antibiotics

Prevent the transpeptidation reaction during peptidoglycan synthesis, degrading the cell wall (ex. penicillin)

Antibiotic resistance + prevention

Bacteria produce an enzyme that destroys B-lactam, preventing cell wall degradation. Prevented by adding a second drug that inhibits the enzyme

Gram positive cells

• One thick outer membrane of peptidoglycan

• Very narrow periplasmic space between the outer membrane and the inner plasma membrane

• LTA + teichoic acids in the peptidoglycan

• Stain purple

Gram negative cells

• An outer membrane of LPS and a thin inner membrane of peptidoglycan

• Varying-width periplasmic space

• Stains pink/red

LPS composition

1. Lipid A

2. Core oligosaccharide

3. Side O chain

Harmfulness of LPS in gram negative cells

• Lipid A induces strong inflammatory responses

• Side O chain can vary dramatically to evade host immune responses + for variation

Entry of nutrients in gram positive vs negative bacteria

• Gram positive: large pores in the peptidoglycan layer

• Gram negative: porin and TonB proteins in the outer membrane, then active transport from the periplasmic space into the cytoplasm

Autotransporters

Proteins that move molecules from the periplasm to the outside of the cell

Type III Secretion System (T3SS)

Single-step transport system, molecular syringe that pushes proteins from the cytoplasm and injects them directly into host cells

Flagellar Assembly

Similar to T3SS components, build flagella by having flagellin subunits travel up the hollow flagellum + add to the tip of the structure

Single step transport systems

Materials never enter the periplasm. Includes T3SS and the flagellar system

Gram staining in gram positive vs. negative cells

Gram positive: alcohol decolouration shrinks the large pores in the outer membrane, locking in the crystal violet

Gram negative: alcohol strips the outer membrane lipids, losing the crystal violet stain

LPS (composition + location + function)

• Composed of lipids and proteins

• Located on outer membrane of gram-negative bacteria, Lipid A portion is embedded while Side O chain sticks out

• Stabilizes membrane + elicits inflammatory response in the human body

Lipoteichoic acid (LTA) (composition + location + function)

• Composed of lipids and proteins

• Located in peptidoglycan layer of gram positive bacteria

• Unknown function, elicits inflammatory response

Peptidoglycan (composition + location + function)

• Composed of protein backbone crosslinked with NAM and NAG

• Located in the outer membrane of gram-positive bacteria and the inner membrane in gram negative bacteria

• Maintains shape and structure to cells

Porins (composition + location + function)

• Composed of proteins

• Embedded in gram-negative outer membrane

• Forms pores that allow for diffusion

TonB-dependent receptors (composition + location + function)

• Composed of proteins

• Embedded in gram-negative outer membrane

• Catalyze high-affinity active transport across the outer membrane

Flagella + distribution

Spiral, hollow, rigid filaments that help a cell move. Can be polar or peritrichous, and inside the periplasm or outside the cell

Convergent evolution and flagella

Flagella evolved independently in bacteria, archaea, and eukarya

Structure of flagella

1. Filament: the long part of the flagella made of flagelin subunits, 5-10 um long

2. Hook protein: connects the filament to the basal body

3. Basal body: disk-like structure that wiggles the filament

Types of movement from flagella

Powered by proton motive force (PMF), can either be directional (a run movement) or nondirectional (a tumble movement)

Chemotaxis

Directional movement of cells by using chemoreceptors to sense changes in concentrations of attractants (positive chemotaxis) or repellants (negative chemotaxis)

Gliding motility

Smooth sliding over a surface, common in cyanobacteria

Twitching motility

Slow, jerky movement using pilli that pull a cell along a surface

Actin-based motility

Cells invade a host cell, polymerize actin to form actin tails, and then propel themselves into adjacent host cells to invade

Adherence molecules

On the surface of bacteria, help them stick to surfaces using pilli or stalks

Sex pilus

Type of pilli used for conjugation (sending a DNA plasmid from one cell to another)

Pili vs fimbriae

Conjugation structures versus adherence structures

Horizontal gene transfer

Movement of DNA from one unrelated cell to another

Stalks

Adherence molecule, extension of the cell envelope tipped with sugar that provides extra surface area for the cell and adherence capability

Capsules

Thick layer of sugars surrounding some cells, providing adhesion, defence against host immunity, and resisting desiccation out via biofilms

Biofilms

A sticky film formed by bacterial capsules that gives cells protection, ex. dental plaque and mold on bathroom surfaces

Surface arrays (S-layers)

Cell armour against bacteriophages, crystalline array of interlocking proteins

Bacterial flagella

• Powered by PMF

• Grows at tip

• Made of flagellin proteins

Archaeal flagella

• Powered by ATP

• Grows at base

• Made of archaellins

Eukaryal flagella

• Powered by ATP dynein motors

• Assembled within the cytoskeleton

• Made of microtubules

Species

Groups of strains sharing common features while differing considerably from other strains

Genus

Group of closely related species

Order of taxonomic groups from broad to specific + what group does bacteria exclude?

Domain > kingdom > phylum > class > order > family > genus > species. Excludes kingdom

Factors bacteria are classified using (6)

1. Cell morphology

2. Colony morphology

3. Growth characteristics

4. Biochemistry

5. Physiology

6. DNA sequence data

Why are bacterial phylogenies and taxonomic classifications revised so often?

New genomic data, better resolution, improved sequencing, more accurate phylogeny, whole-genome insights

Pseudomonadota (formerly proteobacteria)

Extremely diverse gram-negative phylum including:

• Pathogens

• Nitrogen fixers

• Photosynthetic purple bacteria

• Alphaproteobacterium - ancestor of mitochondria

Cyanobacteria

• Photosynthetic bacteria that use light energy to split water, producing O2

• Ancestors of chloroplasts

Culture collections

Newly classified microbes must be deposited in at least 2 culture collections, maintained by the World Federation for Culture Collections

Type strain

A reference specimen deposited in a culture collection

Binomial naming system

Bacteria are named using their genus followed by their species

B-lactamase

Produced by bacteria, destroys B-lactam antibiotics like penicillin

What do NAM and NAG stand for?

N-acetylmuramic acid and N-acetylglucosamine

When carrying out the Gram stain procedure, adding too little or too much alcohol to the sample is a common mistake. Suppose at student added too little alcohol to a sample of Gram-negative bacteria. What would she observe? Why?

The bacteria would appear purple, since all the bacteria would be stained by the crystal violet dye. That’s because Gram-negative bacteria do not retain the stain due to their thin peptidoglycan layer. Therefore, using too little alcohol would not remove the stain.

What is the main function of peptidoglycan (cell wall)?

Protecting against osmotic stress

Conjugation

Transfer of DNA from one bacteria cell to another via a sex pilus