17. SOS response in E. coli

Question 1

What are the two pathways used to repair ssDNA gaps and dsDNA breaks by recombination?

Answer 1

ssDNA gaps: RecFOR
dsDNA breaks: RecBCD

Both load RecA onto ssDNA - search homologous fragment for recombination

Question 2

Before which event DNA damage must be repaired?

Answer 2

DNA damage must be repaired before cell division - not to pass defective DNA - if DNA damage detected - must be repaired quickly or cell cycle must be stopped

Question 3

Why is overproduction of DNA damage repair proteins a problem?

Answer 3

Overproduction of DNA damage repair proteins:
- inefficient cell resource allocation
- if repair proteins active when not needed - can damage the cell -> production must be tightly regulated

Question 4

How is the repair response of E. coli DNA damage called?

Answer 4

SOS response

Question 5

What is the SOS response?

Answer 5

SOS response - DNA damage repair response system in E. coli

SOS regulon - LexA transcriptional repressor controls a group of DNA repair genes

Question 6

Where are SOS genes located?

Answer 6

In E. coli chromosome - plasmid - scattered across all chromosome not in one locus - all have different functions

Question 7

What is the mechanism of controlling SOS gene expression?

Answer 7

Control of SOS gene expression:
- LexA - transcriptional supressor (TF) of SOS genes
- RecA - protease - cleaves LexA - SOS gene expression started

Question 8

Explain SOS response when there is no DNA damage

Answer 8

No DNA damage - no RecA protease recruitment - LexA bound to SOS gene promoter - no expression of SOS genes

Question 9

Explain SOS response upon DNA damage

Answer 9

DNA damage - RecFOR/RecBCD recruits RecA - RecA degrades LexA - SOS gene promoter free - SOS genes expressed - DNA damage repair attempted

Question 10

How does LexA supress SOS gene transcription?

Answer 10

LexA binds on SOS gene promoter - specific sequence - LexA box - overlaps with pol binding site: when LexA bound - pol can’t bind -> no expression

Question 11

Because SOS genes are scattered across chromosome, what determines the sequence at which SOS genes are expressed?

Answer 11

The sequence of SOS gene expression depends on LexA binding strength - LexA box sequence:
- if sequence more different from template LexA - bound weakly - early expression
- if sequence more similar to template LexA - bound strongly - late expression

The more DNA damage - more RecA - more LexA degraded - more SOS genes expressed

Question 12

What are the positive and negative feedback loops used for in SOS response?

Answer 12

To tightly control the amount of gene expression

Question 13

What are the roles of SOS genes?

Answer 13

Roles of SOS genes:
- HR
- nucleotide excision repair
- pol
- other DNA action
- cell division
- SOS regulator (LexA)
- toxicity

Question 14

What is the timeline of SOS response in terms of expressed SOS gene role?

Answer 14

Early SOS response - fast + faithfull:
- pol (non-harmful)
- HR
- nucleotide excision repair
- other action on DNA
- LexA expression

If the damage still not repaired - further more serious measures - last resort to survive

Late SOS response - higher danger to the cell:
- stop cell division
- toxicity
- pol (harmful)

If not repaired by late SOS response - cell dies

Question 15

What are the consequences of SOS response?

Answer 15

SOS response consequences in the cell:
- HR (gene dosage - integration of new genes - ex: antimic. resistance)
- increased mutation rate (if deleterious - cell dies)
- stopped cell cycle (bacterial colonization stopped - persister cells/dormancy can be induced)
- produced toxic molecules

Question 16

Quiz 1

Answer 16

Question 17

Quiz 2

Answer 17

Question 18

Quiz 3

Answer 18

Question 19

Quiz 4

Answer 19

Question 20

Define nucleotide excision repair

Answer 20

Nucleotide excision repair (NER) - DNA repair mechanism - DNA damage occurs constantly because of chemicals, radiation, other mutagens

Question 21

Define consensus sequence

Answer 21

The template sequence against which other are compared

Question 22

Define what is a regulon

Answer 22

Regulon - group of genes that are regulated as a unit by the same regulatory gene

Question 23

Define error-prone polymerase

Answer 23

A pol in late SOS response that is used as last resort to save the cell - effective but error-prone

Question 24

Define ribosome binding site

Answer 24

Ribosome binding site (RBS) - when mRNA transcribed - RBS where ribosome binds on mRNA to translate SOS genes

Question 25

Define operon

Answer 25

Operon - gene unit which regulates other genes responsible for protein synthesis

Question 26

Define translational synthesis

Answer 26

Translational synthesis (translation) - protein synthesized from the information contained in mRNA

Question 27

Define transcriptional repressor

Answer 27

A TF which binds and represses transcription instead of promoting it - ex prevents pol binding - ex LexA

Question 28

What are -35/-10 boxes?

Answer 28

-35 site: start of pol binding fragment on SOS gene promoter
-10 site: start of LexA box - binding site fo LexA on SOS gene promoter

LexA binding site interferes with pol binding site - when LexA bound - polymerase can’t bind

Question 29

What is LexA box?

Answer 29

LexA box - LexA binding site on SOS gene promoter