Lecture 11

Question 1

What is a core genome?

Answer 1

• The essential bacterial genes on a chromosome
• Genes are conserved in all members of a species
• e.g. replication, cell membrane formation

Question 2

What is an accessory genome?

Answer 2

• Located on a plasmid, transposon, chromosomal islands
• Non-essential genes of variable occurrence in species
• Acquired through horizontal transmission

Question 3

What kind of genetic element is a plasmid?

Answer 3

An extrachromosomal genetic element

Question 4

What do plasmids contribute to?

Answer 4

• Bacterial evolution

- Genetic plasticity

Question 5

Are plasmids capable of autonomous replication?

Answer 5

Yes

Question 6

What do plasmids with AbR genes encode?

Answer 6

Enzymes that modify and degrade antibiotics

Question 7

What are AbR genes on plasmids carried on?

Answer 7

Transposons

Question 8

What functions must a plasmid carry out for survival?

Answer 8

1. Replicate
2. Segregate = ensure each daughter cell receives at least one copy upon division
3. Keep host happy
   - constrain metabolic load by regulating copy number
4. Keep host controlled = kill of cells that kick them out
5. Spread = via conjugation

Question 9

How do Large Plasmids regulate copy number?

Answer 9

They have a low copy number, only have 1-5 copies per cell

Question 10

How do Small Plasmids regulate copy number?

Answer 10

They have a high copy number, about 10-50 copies per cell

Question 11

How do low copy plasmids partition plasmids at cell division?

Answer 11

Use specialised molecular machinery to ensure each daughter cell gets a plasmid

Question 12

How do high copy plasmids partition plasmids at cell division?

Answer 12

Use random partitioning, as long as copy number is 15< the chance of non-inheritance is reduced

Question 13

How is the Par M system (low copy plasmids) accomplished?

Answer 13

By two proteins (Par M and R) and a centromere-like DNA site (par s)

Question 14

What is Par M?

Answer 14

An actin-like protein that polymerases to form filaments

Question 15

What is Par R?

Answer 15

DNA binding adaptar protein

Question 16

What is Par s?

Answer 16

A centromere-like region

Question 17

Describe the steps in the Par M system

Answer 17

1. Replicated plasmids are paired by Par R bound to Par s, forming a partitioning complex
2. Complex forms a nucleation point for Par M filament
3. Continuous addition of Par M to filament poles provides force for movement of plasmids to opposite cell poles
4. When plasmids reach the poles, the filament depolymerises
   (1. Replication, 2. Search/Capture, 3. Elongation, 4. Depolymerisation)

Question 18

What is plasmid DNA replication controlled by?

Answer 18

By plasmid encoded inhibitor that acts on the OriV

Question 19

In plasmid DNA replication, as cell size increases what happens?

Answer 19

The inhibitor concentration decreases and plasmid replication is initiated

Question 20

In plasmid DNA replication, replication results in….

Answer 20

Further copies of the inhibitor gene and more inhibitor which limits plasmid replication again

Question 21

What do incompatible plasmids share?

Answer 21

The same regulatory mechanisms and are subject to each other’s inhibitor
->one eventually gains upper hand and eliminates the other

Question 22

What does the rom (rop) protein encode?

Answer 22

Encodes a protein that regulates plasmid copy number

Question 23

Describe the control of plasmid replication in ColE1

Answer 23

• It’s mediated by plasmid-encoded anti-sense RNA
  1. RNA II binds to ColE1 OriV to initiate replication
  2. In presence of Rop protein, RNA I binds to RNA II and prevents it binding to OriV
• > REPLICATION STOPS

3. Formation of a persistant RNA II / DNA Hybrid is required for initiation of replication
   - >’persistant’ because the RNA stays in the cell for a while, instead of leaving
4. At critical Rop concentration a dimer is formed
   - >secondary RNA structure (G’s) allows it to form the structure and attach the DNA

Question 24

What is the control of Plasmid replication in F mediated by?

Answer 24

A protein binding to repeated sequences

Question 25

In the control of plasmid rep (F) what happens at low concentrations of Rep A?

Answer 25

Rep A binds to OriV and initiates replication

Question 26

In the control of plasmid rep (F) what happens at high concentrations of Rep A?

Answer 26

Rep A also binds to iteron sequences and ‘hand-cuffs’ plasmids together this prevents replication until plasmids are separated at cell division