Lc6: bacterial evolution

Question 1

environmental pressure by antibiotics

Answer 1

• Immense use by human (>73billion pills per year) and agriculture (>63 million kg)
• Environmental pollution due to production in China and India
  o Extreme amounts of antibiotics get wasted in water near the production plants
• In downstream waters of these dumping sites bacteria with resistance genes can be found

Question 2

AMR spreading facotrs

Answer 2

o (mis)use for medical purposes
o Use in agriculture
o Spilling/pollution into environment
o Global travel

Question 3

HGT

Answer 3

o Conjugation
o Transformation
o Transduction
o Vesiduction

Question 4

conjugation

Answer 4

• The transfer of DNA by direct cell-to-cell contact
• Enabled by conjugative apparatus (sex pili and type IV secretion system)
  o Encoded by the ‘Fertility(F) factor’
• Primary mechanism of plasmid transfer

Question 5

F-factor mediated

Answer 5

1. The sex pilus is used to establish contact between the F+ and F− cells
2. Once contact is made, the pilus retracts, bringing the cells into close physical contact.
3. The F+ cell prepares for DNA transfer by assembling a type IV secretion system, repurposing many of the proteins in the sex pilus
   a. The term sex pilus refers to the extracellular structure, while the membrane-bound components are termed the type IV secretion system (T4SS)
4. As the F plasmid is transferred, it is also copied using a process called rolling-circle replication
   a. During conjugation, rolling-circle replication is initiated by the relaxosome, a complex of proteins encoded by the F factor

Question 6

Hrf mediated

Answer 6

• The F Factor can also be integrated into the donor’s chromosome  Hfr conjugation
  o Rather than transferring just itself, the F factor also directs the transfer of the host chromosome
  o If the cells remain connected, the entire chromosome with the rest of the integrated F factor will be transferred; this takes about 100 minutes to accomplish.
  o However, the connection between the cells usually breaks before this process is finished.

Question 7

transformation

Answer 7

• Uptake of circular or linear DNA from the environment outside the cell by a competent cell (complex)
  o Not random DNA there are specialised protein involved

Question 8

transformation

Answer 8

• Uptake of circular or linear DNA from the environment outside the cell by a competent cell (complex)
  o Not random DNA there are specialised protein involved

Question 9

transduction

Answer 9

• HGT mediated by viruses (bacteriophages)
• Common occurrence in nature (aquatic)
• Virulent phages -> lytic phase
• Temperate bacteriophages -> insertion into genome – lysogeny
• General transduction vs. specialized transduction

Question 10

general transduction

Answer 10

• Random inclusion of bacterial DNA in phage head after lytic cycle
• Transducing phage may deliver bacterial genes to recipient, phage unable to function (missing genes)

Question 11

specialised transduction

Answer 11

Result of error during excision of lysogenic cycle of temperate phage
- Inclusion of bacterial host DNA in phage during excision
- Phage also defective

Question 12

vesiduction

Answer 12

• Extracellular Membrane Vesicles
• Secreted from the (outer) cell membrane
• Wide range of functions:
  o HGT
  o Toxins
  o DNA
  o Signalling
  o Etc.
• Largely unexplored mechanism

Question 13

mobile genetic elements

Answer 13

• Insertion sequences
• Transposons
• Plasmids
• Integrative and conjugative elements

Question 14

insertion sequence

Answer 14

• Transposase: excision and movement of IS
• IR: inverted repeats (15-25 bp) – recognition site for transposase
• DR: direct repeats – part of target genome, not IS
• IS does not contain additional genes

Question 15

transponson

Answer 15

• Transposons carry central region, unrelated to transposition (e.g. antibiotic resistance genes)
• Composite and unit types
  o Composite  resistance gene flanked by insertion sequences
  o Unit  lacks the flanking IS and has its own resolvase and has also carrier genes
   Resolvase: release the two replicons after replicative transposition

Question 16

integrative and conjugative elements

Answer 16

• Mobile genetic elements integrated into a host genome
• Passively propagated during chromosomal replication
  o excision, production of conserved conjugation machinery (type IV secretion system) –> conjugation
• cannot remain in an extrachromosomal form in the cytoplasm (in contrast to plasmids and phages

Question 17

virulence factors

Answer 17

• Virulence is the degree of harm inflicted on its host
• To infect a host and subsequently cause disease, specific events must take place.
  1. Transmission, invasion - adhesion and invasion/dissemination factors
  2. Outcompete resident microbiota & survive the host defence mechanisms - producing a variety of molecules (e.g., antiphagocytic factors)
  3. Cause disease - produces molecules (toxins) that directly damage host cells or stimulates the immune cells to destroy infected tissue
• Several of these factors/molecules are delivered via Secretion Systems

Question 18

T3SS

Answer 18

• Used by pathogens to inject proteins into eukaryotic host cell * One-step system
• A.k.a. injectosomes
• Injected content: effector proteins
  o Alter cell cytoskeleton, signal transduction pathways or other cellular processes
  o E.g. tight-junction (TJ) disruption  EPEC and EHEC (leads to diarrhoea and tissue invasion)

Question 19

T4SS

Answer 19

• Most commonly used for HGT
• One-step system
• Conjugation Machinery encoded by F-Factor is a T4SS

Question 20

T6SS

Answer 20

• Contractile weapons
• Used to deliver toxins to bacterial and eukaryotic cells
• One-step system
• Example: Vibrio cholerae Nutrient competition with other bacteria in aquatic environments
  o When ingested by humans  competition with gut microbiota, infection (cholera)

Question 21

adhesion factors

Answer 21

• microbial cell wall is often covered with adherence structures (adhesins)
• Pili/fimbriae
  o Allow bacteria to colonize environmental surfaces or cells and resist flushing
  o Adhesive tip at end of fimbriae - structure corresponding to specific glycoprotein or glycolipid receptors on a host cell.
• Capsular material
  o Aid in the attachment to tissue surfaces
• Adhesion molecules / membrane proteins
  o Recognize many different elements of host-cell surfaces

Question 22

invasion/dissemination factors

Answer 22

• From localized infection to infecting other tissues:
  o Attacking the extracellular matrix and basement membranes of body surfaces and intestinal linings (e.g. collagenase or hyaluronidase)
  o Degrading carbohydrate-protein complexes between cells or on the cell surface (the glycocalyx). E.g. mucus degradation
  o Disrupting the host cell surface. E.g. tight junction disruption (see also type III secretion system above)

Question 23

evading immune system/outcompeting others

Answer 23

• Killing of other bacteria (e.g. via T6SS)
• Production of capsules that resemble host tissue
  o Escape of detection
  o Prevent deposition of complement system
• Production of proteases that degrade host proteins such as IgA
• Production of biofilms (promotes HGT conditions!)
• Iron scavenging (siderophores)
  o Bind ferric iron (Fe3+) and supply it to the cell

Question 24

disease causing

Answer 24

• Exotoxins:
  o Released into host tissues as the bacterial pathogen metabolizes
  o Often encoded by genes on plasmids or prophages
  o Superantigens – stimulate up to 30% of T-cells: cytokine storm
• Endotoxins
  o Bound to the bacterium and is released when the microorganism lyses (LPS !)