Lecture 17 - The SOS repsonse In E.coli

Question 1

What does an organism need to do after DNA damage?

Answer 1

Efficiently and swiftly repair it so the cell cycle can continue. The cell cycle will pause so the damage is not given to the next generation

Question 2

How can the stress response be an issue?

Answer 2

Can sometimes lead to errors and overproduction if repair proteins can be a problem for the cells as you are using up all the source and if it’s not needed it could cause harm

Question 3

The SOS response - what is a regulon?

Answer 3

Group of genes/operons that are under the control of the same regulator (LexA)

Question 4

Is the sos response specific?

Answer 4

Yes

Question 5

Do all regullon have different functions and can move throughout the cell?

Answer 5

Yes but they are all involved in cell survival

Question 6

Where is the sos regulator found in the chromosome?

Answer 6

90 minutes

Question 7

Are all regulons spread across the cell?

Answer 7

Yes

Question 8

If there is no DNA damage where does the LexA bind?

Answer 8

Specific regions in the promotor of the SOS genes this is a LexA box or a SOS box

Question 9

Is LexA a repressor?

Answer 9

Yes

Question 10

What does the LexA gene do when bound to the SOS promotor?

Answer 10

It impedes transcription

Question 11

Where is the LexA box near?

Answer 11

The RNA polymerase binding site

Question 12

What happens when a LexA dimer binds to the LexA box which is in an RNA polymerase binding site?

Answer 12

It interferes with RNA polymerase repressing the expression of the sos genes

Question 13

When the sos response is not needed are the sos genes expressed?

Answer 13

No

Question 14

Do most genes have a basal expression level and what does this mean?

Answer 14

even when turned off they will still excrete a minimum expression

Question 15

What genes would be expressed first from a Lexa box?

Answer 15

If a lexA box is bound to a sequence of DNA that is most different to its consensus sequence of DNA as this will be a weaker binding.

Question 16

Are genes which are expressed later stronger in a LexA box?

Answer 16

Yes as they bind more tightly to the consensus strand as there is more sequences in common

Question 17

What is also important in the timing of expression of genes and also the strength of the genes?

Answer 17

The location and their place in the promotor

Question 18

The SOS system - what happens in a double strand break?

Answer 18

RECBCD processes DNA and loads RECA recombinase onto the strand to make a recA ss DNA filament.

The active RECA filament can then act of Lexa

Question 19

How does the active RECA filament act on Lexa?

Answer 19

Acts as a co-protease and induces self-cleavage of cytoplasmic LexA.

Question 20

What happens to LexA once it is cleaved?

Answer 20

Cytoplasmic LexA is further degraded by cytoplasmic proteases and the concentration of LexA decreases meaning less LexA can bind to the LexA boxes the most different from the consensus sequence

Question 21

What does the absence of the LexA boxes facilitate?

Answer 21

Allows the RNA polymerase into the promotor and the transcription of the genes increase.

Question 22

What does the level of SOS response activate?

Answer 22

The transcription of genes expressed in early SOS response

Question 23

What would happen if the damage was not repaired and RECA was still present?

Answer 23

The concentration of cytoplasmic LexA decreases further leading to the expression of more genes. The longer the cell experiences DNA damage the more SOS genes are transcribed until the expression of later SOS genes

Question 24

Why are feedback loops used?

Answer 24

They regulate and can amplify the response.

Question 25

What is a positive feedback loops role?

Answer 25

To amplify if the problem isn’t solved

Question 26

What is the negative feedback loops response?

Answer 26

To stop the response if the problem is solved

Question 27

How does the SOS response create feedback loops?

Answer 27

The direct influence of LexA and recA

Question 28

What further regulates the feedback loop?

Answer 28

Other proteins as some stabilise RecA ssDna and some destabilise it.

Question 29

What does nucleotide excision repair do?

Answer 29

Faithfully fixes nucleotides onto broken DNA strands

Question 30

What do all the genes involved in the SOS response do?

Answer 30

homologous repair
Nucleotide excision repair
Polymerase
Other action on DNA
Cell division
SOS regulators
Toxic

Question 31

How does translation synthesis work when repairing DNA?

Answer 31

They use specific polymerase to replicate through DNA lesions this can be either faithful or not

Question 32

What is the general timeline of SOS response? early response

Answer 32

During early response the integrity of the DNA is trying to be kept and things such as polymerase high-fidelity, homologous recombination and nucleotide excision repair takes place. This needs to be fast and faithful

Question 33

What is the general timeline of SOS response? What happens if the response has repaired the DNA?

Answer 33

More LexA is produced to stop the response if damage is repaired. However if its not the late response takes place

Question 34

What is the general timeline of SOS response? The late response?

Answer 34

The cell cycle needs to be stopped at this point and so the cell uses toxic genes which impair cell division, cell growth and DNA replication. The SOS response ten starts sending out error prone polymerase high-fidelity to try and repair the cell through translation synthesis - this is slow and can produce mutations

Question 35

What are the consequences of the SOS response?

Answer 35

Homologous recombination = genome rearragement

Increase mutation rate

Stop cell cycle

Question 36

What induces the SOS response?

Answer 36

Horizontal gene transfer

Question 37

Why could slowing down cell cycle be good?

Answer 37

Antimicrobials target fast growing cells

Question 38

What do Antimicrobials do which would start the SOS response?

Answer 38

They damage DNA