DNA Mutagenesis & DNA Repair
DNA MUTAGENESIS & DNA REPAIR............................................................................................................... 1
DEFINITIONS.........................................................................................................................................................3
MUTATIONS:................................................................................................................................................. 3
GENETIC VARIATION IN BACTERIA.............................................................................................................................3
CONSEQUENCES OF MUTATIONS...............................................................................................................................3
CAUSES OF MUTATIONS..........................................................................................................................................4
Spontaneous mutations (From spontaneous errors):.....................................................................................4
Metabolism............................................................................................................................................................... 4
Replication errors......................................................................................................................................................4
Tautomerism:............................................................................................................................................................ 4
Depurination:............................................................................................................................................................ 4
Insertion of DNA via Mobile Genetic Elements.........................................................................................................4
Induced mutations (From induced errors):.....................................................................................................4
TYPES OF MUTANTS:.............................................................................................................................................. 6
BACTERIAL GENOTYPE NOMENCLATURE.....................................................................................................................7
MUTANT ENRICHMENT...........................................................................................................................................8
Penicillin Enrichment Method to isolate Auxotrophic mutants......................................................................8
MUTANT IDENTIFICATION........................................................................................................................................8
AMES TEST FOR MUTAGENICITY...............................................................................................................................9
Ames Assay:....................................................................................................................................................9
Mutagenicity Index & Ratio:...........................................................................................................................9
TRANSCRIPTION AND TRANSLATION.........................................................................................................................10
CLASSES OF MUTATIONS............................................................................................................................. 10
MACROLESIONS...................................................................................................................................................10
MICROLESIONS....................................................................................................................................................10
Base substitutions:..................................................................................................................................................10
Frameshift mutations:.............................................................................................................................................11
SUPPRESSOR MUTATIONS.....................................................................................................................................11
tRNA Suppressor Mutations:........................................................................................................................11
DNA Damage................................................................................................................................................12
CELLULAR DNA REPAIR RESPONSES............................................................................................................. 13
DAMAGE REVERSAL............................................................................................................................................. 13
Enzymatic Photoreactivation (Light Repair).................................................................................................13
Mechanisms of action:............................................................................................................................................13
Methyltransferases.......................................................................................................................................13
DAMAGE EXCISION.............................................................................................................................................. 14
Nucleotide excision Repair (NER).................................................................................................................14
Regulation of NER genes/operons in bacteria.........................................................................................................14
UvrABC NER:............................................................................................................................................................ 14
UV Survival Curves:.................................................................................................................................................14
Xeroderma Pigmentosum.......................................................................................................................................15
TC-NER: (Transcription-Coupled NER).....................................................................................................................15
Base Excision Repair (BER)...........................................................................................................................15
Mechanism:............................................................................................................................................................. 16
Methyl-directed Mismatch Repair................................................................................................................16
Mechanism:............................................................................................................................................................. 16
Proof that DNA methylation is needed for mismatch recognition:.........................................................................16
Hereditary Nonpolyposis Colorectal Cancer:...........................................................................................................17
DAMAGE TOLERANCE...........................................................................................................................................17
SOS Response................................................................................................................................................17
Damage inducible genes and function of products:................................................................................................18
Activation of RecA:..................................................................................................................................................18
Mechanism of sequential response:........................................................................................................................18
Transcriptional regulation via Regulon....................................................................................................................19
Relationship between Induced and Un-induced state:............................................................................................19
,DNA Mutagenesis & DNA Repair
SOS Response: Homologous Recombination (Middle Response).................................................................19
RecBCD Pathway:....................................................................................................................................................20
SOS Response: Error-prone DNA Repair.......................................................................................................20
Non-homologous End-Joining (NHEJ)...........................................................................................................20
Repairs double-stranded breaks (DSB) in DNA.............................................................................................20
Involves three main proteins (Ku70, Ku80, DNA PKcs) and accessory proteins...........................................20
DSB is recognized by Ku dimer (Ku70–Ku80) and DNA-PKcs........................................................................20
The dimer and proteins above allow the two DNA ends to be repaired (synapsed)....................................20
Other accessory proteins are recruited and DNA-PKcs allows accessory proteins to process DNA ends....20
Overhanging nucleotides at end that do not have complimentary nucleotide to pair are ‘cut back’ (resect)
and ends ligated by DNA ligase IV................................................................................................................20
Resection results in NHEJ losing DNA – error in DNA...................................................................................20
, DNA Mutagenesis & DNA Repair
Definitions
Genotype:
- Genetic information on genome
- Includes plasmids and transposons in bacteria (Metagenome)
Phenotype:
- Physical characteristics in that environment
- Genotype + environment = phenotype
Wildtype:
- Not altered with respect to the particular genotype or phenotype being examined
- Genotype without any mutations
Mutagen:
- A substance or agent that induces heritable change in cells or organisms
Carcinogen:
- Mutagen that induces unregulated growth processes in cells or tissues of
multicellular animals, leading to cancer (tumor).
- Carcinogenesis often results from mutagenic event
Genotoxicity:
- Describes the property of chemical agents to cause damage to genetic information
within a cell causing mutation which are not necessarily heritable.
- All mutagens are genotoxic, whereas not all genotoxic substances are mutagenic.
Mutations:
An inherited change in genetic information
- DNA susceptible to change
- Plus factor – driving force in evolution
- Minus factor – too much change is lethal
Genetic Variation in bacteria
- Rapid growth
o Increase from 1- 109 in 12 h
- Approximately 1 in every 109 cells is a spontaneous mutant (no external agent
involved to mutate it)
- In theory, can see 1 mutation event in every 12h
- Changes are easily seen (because they are haploid, genotype is linked to phenotype)
- We can increase mutation rate using external agents
Consequences of mutations
1. General value
DNA MUTAGENESIS & DNA REPAIR............................................................................................................... 1
DEFINITIONS.........................................................................................................................................................3
MUTATIONS:................................................................................................................................................. 3
GENETIC VARIATION IN BACTERIA.............................................................................................................................3
CONSEQUENCES OF MUTATIONS...............................................................................................................................3
CAUSES OF MUTATIONS..........................................................................................................................................4
Spontaneous mutations (From spontaneous errors):.....................................................................................4
Metabolism............................................................................................................................................................... 4
Replication errors......................................................................................................................................................4
Tautomerism:............................................................................................................................................................ 4
Depurination:............................................................................................................................................................ 4
Insertion of DNA via Mobile Genetic Elements.........................................................................................................4
Induced mutations (From induced errors):.....................................................................................................4
TYPES OF MUTANTS:.............................................................................................................................................. 6
BACTERIAL GENOTYPE NOMENCLATURE.....................................................................................................................7
MUTANT ENRICHMENT...........................................................................................................................................8
Penicillin Enrichment Method to isolate Auxotrophic mutants......................................................................8
MUTANT IDENTIFICATION........................................................................................................................................8
AMES TEST FOR MUTAGENICITY...............................................................................................................................9
Ames Assay:....................................................................................................................................................9
Mutagenicity Index & Ratio:...........................................................................................................................9
TRANSCRIPTION AND TRANSLATION.........................................................................................................................10
CLASSES OF MUTATIONS............................................................................................................................. 10
MACROLESIONS...................................................................................................................................................10
MICROLESIONS....................................................................................................................................................10
Base substitutions:..................................................................................................................................................10
Frameshift mutations:.............................................................................................................................................11
SUPPRESSOR MUTATIONS.....................................................................................................................................11
tRNA Suppressor Mutations:........................................................................................................................11
DNA Damage................................................................................................................................................12
CELLULAR DNA REPAIR RESPONSES............................................................................................................. 13
DAMAGE REVERSAL............................................................................................................................................. 13
Enzymatic Photoreactivation (Light Repair).................................................................................................13
Mechanisms of action:............................................................................................................................................13
Methyltransferases.......................................................................................................................................13
DAMAGE EXCISION.............................................................................................................................................. 14
Nucleotide excision Repair (NER).................................................................................................................14
Regulation of NER genes/operons in bacteria.........................................................................................................14
UvrABC NER:............................................................................................................................................................ 14
UV Survival Curves:.................................................................................................................................................14
Xeroderma Pigmentosum.......................................................................................................................................15
TC-NER: (Transcription-Coupled NER).....................................................................................................................15
Base Excision Repair (BER)...........................................................................................................................15
Mechanism:............................................................................................................................................................. 16
Methyl-directed Mismatch Repair................................................................................................................16
Mechanism:............................................................................................................................................................. 16
Proof that DNA methylation is needed for mismatch recognition:.........................................................................16
Hereditary Nonpolyposis Colorectal Cancer:...........................................................................................................17
DAMAGE TOLERANCE...........................................................................................................................................17
SOS Response................................................................................................................................................17
Damage inducible genes and function of products:................................................................................................18
Activation of RecA:..................................................................................................................................................18
Mechanism of sequential response:........................................................................................................................18
Transcriptional regulation via Regulon....................................................................................................................19
Relationship between Induced and Un-induced state:............................................................................................19
,DNA Mutagenesis & DNA Repair
SOS Response: Homologous Recombination (Middle Response).................................................................19
RecBCD Pathway:....................................................................................................................................................20
SOS Response: Error-prone DNA Repair.......................................................................................................20
Non-homologous End-Joining (NHEJ)...........................................................................................................20
Repairs double-stranded breaks (DSB) in DNA.............................................................................................20
Involves three main proteins (Ku70, Ku80, DNA PKcs) and accessory proteins...........................................20
DSB is recognized by Ku dimer (Ku70–Ku80) and DNA-PKcs........................................................................20
The dimer and proteins above allow the two DNA ends to be repaired (synapsed)....................................20
Other accessory proteins are recruited and DNA-PKcs allows accessory proteins to process DNA ends....20
Overhanging nucleotides at end that do not have complimentary nucleotide to pair are ‘cut back’ (resect)
and ends ligated by DNA ligase IV................................................................................................................20
Resection results in NHEJ losing DNA – error in DNA...................................................................................20
, DNA Mutagenesis & DNA Repair
Definitions
Genotype:
- Genetic information on genome
- Includes plasmids and transposons in bacteria (Metagenome)
Phenotype:
- Physical characteristics in that environment
- Genotype + environment = phenotype
Wildtype:
- Not altered with respect to the particular genotype or phenotype being examined
- Genotype without any mutations
Mutagen:
- A substance or agent that induces heritable change in cells or organisms
Carcinogen:
- Mutagen that induces unregulated growth processes in cells or tissues of
multicellular animals, leading to cancer (tumor).
- Carcinogenesis often results from mutagenic event
Genotoxicity:
- Describes the property of chemical agents to cause damage to genetic information
within a cell causing mutation which are not necessarily heritable.
- All mutagens are genotoxic, whereas not all genotoxic substances are mutagenic.
Mutations:
An inherited change in genetic information
- DNA susceptible to change
- Plus factor – driving force in evolution
- Minus factor – too much change is lethal
Genetic Variation in bacteria
- Rapid growth
o Increase from 1- 109 in 12 h
- Approximately 1 in every 109 cells is a spontaneous mutant (no external agent
involved to mutate it)
- In theory, can see 1 mutation event in every 12h
- Changes are easily seen (because they are haploid, genotype is linked to phenotype)
- We can increase mutation rate using external agents
Consequences of mutations
1. General value
