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Year 3: SGE > LGT > Flashcards

LGT Flashcards

1
Q

What are the three mechanisms for LGT?

A
  1. Transduction
  2. Conjugation
  3. Transformation
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2
Q

What is transduction?

A

Infection by bacteriophages, which are selfish

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3
Q

What is conjugation?

A

Transfer and copy of plasmids between cells

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4
Q

What is transformation?

A

Uptake of naked DNA from the environment

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5
Q

How many ‘house-keeping’ genes does the bacterial genome contain?

A

2000

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6
Q

How many extra genes does the bacterial genome contain?

A

18,000

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7
Q

Can bacteria carry more than one plasmid?

A

Yes

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8
Q

Can bacteria carry different types of plasmids?

A

Yes

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9
Q

How many plasmids can E. coli carry?

A

0-11

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10
Q

How many different types of E. coli plasmids are there?

A

100s

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11
Q

In conjugation, where is the transfer machinery?

A

Carried by the plasmid

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12
Q

Is there a risk involved in conjugation?

A

Yes, a high risk of segregational loss of the plasmid during transfer

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13
Q

There are two types of selection that act on plasmids. What is individual selection?

A

Acts on the fitness of the plasmid itself

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14
Q

What 3 factors favour increased plasmid copy number under individual selection?

A
  1. Plasmid avoids segregational loss
  2. Plasmid outcompetes other plasmids
  3. There is a high probability of conjugation between cells
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15
Q

There are two types of selection acting on plasmids. What is group selection?

A

Acts on the fitness of the host

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16
Q

Under group selection on plasmids, when does the fitness of the host decrease? Why?

A

With high copy number as it is a metabolic burden

17
Q

Who looked at the effects of copy number in yeasts? Which genus?

A

Harrison et al., 2012

Saccharomyces yeasts

18
Q

Harrison et al. 2012:

Which plasmid did they study in Saccharomyces? What does it contain?

A

2 μm

Encodes about 4 genes

19
Q

Harrison et al., 2012:

What was the fitness burden of 2 μm plasmids per copy?
Can it be stably maintained?

A

0.17% reduction in fitness per copy

No, cost is higher than expected

20
Q

What does policing in plasmids involve?

A

Inhibitors (of replication) and obedience (affinity to inhibitor)

21
Q

What is the point of a plasmid policing itself?

A

It can maintain lower copy numbers, creates a trade of between selfishness and longevity.

If plasmid holds back in copy number NOW, it will not decrease the fitness of the host too much and can be maintained for longer.

22
Q

Who described how RM systems work?

A

Kobayashi, 2001

23
Q

Kobayashi, 2001:

What is an RM system?

A

Restriction-modification

Restriction enzyme cuts and modification enzyme modifies, e.g. methylation

Self DNA is methylated to protect from cutting, restriction enzyme cuts ‘other’ DNA

24
Q

Who described the hok/sok system?

A

Gerdes et al., 1990

25
Q

Gerdes et al., 1990:

Where is the hok/sok system located?
Which organism is it found in?
What does it do?
How does it work?
Is the plasmid selfish?
A

On plasmid R1
E. coli
It is a post-segregational killing mechanism; one of the two daughter cells inherit it, this daughter can produce sok and will live. Other daughter without the plasmid dies because they do not have the antitoxin to hok.
Hok is a cell killing protein, sok is the antitoxin (antisense RNA of hok)
Yes, kills competitor hosts that do not possess the plasmid, more resources for its host

26
Q

What are the possible benefits of transformation? List 5.

A
  1. Food
  2. DNA repair
  3. Sex and recombination
  4. Gather new, locally-adapted alleles from the pan-genome
  5. Gene loss
27
Q

How can gene loss be achieved from transformation?

A

Recombine flanking markers that lack content, can streamline the genome = faster replication and loss of expensive protein synthesis.

28
Q

What is a cost of transformation?

A

Could uptake damaged DNA or selfish elements.

29
Q

Where does the DNA come from in transformation? List 3.

A
  1. Dead cells, DNA may be faulty
  2. Selfish elements
  3. Cooperation from clonal relatives who have released DNA into the environment
30
Q

Who looked at uptake specificity in transformation?

A

Mell et al., 2012

31
Q

Mell et al., 2012:

What is uptake specificity?

A

Competent cells show strong preference for ‘uptake sequences’ that are dramatically overrepresented sequences in their genomes.

32
Q

Mell et al., 2012:

What organism was studied?
What did they find?
How was DNA uptaken?
How much more efficient is this than random uptake?
What else did they find?
A

H. influenzae
It had a 9bp uptake sequence at the membrane
H. infuenzae has a double membrane that DNA cannot easily cross, DNA binds at uptake sequences on the membrane and is pulled across the cell wall.
10-100x more efficient
Uptake specificity is species-specific, Neisseria has a different uptake sequence

Year 3: SGE (11 decks)

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