ROS, RNI, DNA Damage
and Repair Signaling
Lynn Harrison, Ph.D.Department of Molecularand Cellular Physiology
Endogenous Cellular Factors That Damage DNA
• Replication errors– e.g. imbalance in the nucleotide pools– result in mismatch
• DNA instability– deamination of bases– depurination/depyrimidination of DNA
• loss of base
• Reactive oxygen and nitrogen species– DNA oxidation and deamination
Types of DNA Damage
• Base Damage
• Loss of bases - abasic or apurinic sites
• Strand breakage
• Protein-DNA cross-links
• DNA-DNA cross-links
Reactive oxygen species• Produced by normal cellular metabolism
• Mitochondria utilize ~85% O2 in cell and are a major source of ROS
• Damage DNA, protein and lipid.
• Some forms in cell are:– Hydrogen peroxide (H2O2)
– Superoxide radical (O2•-)
– Nitric oxide (•NO)– Hydroxyl radical (HO•)
• Fenton Reaction– Metal-catalyzed formation of HO• radicals. This
reaction can function in a redox cycle in which a transition metal ion transfers electrons from donors.
DNA(FeII) + H2O2 DNA(FeIII) + OH + OH-
• Hydroxyl radicals– Small modifications to bases, many types/base
– Single and double strand breaks
– Abasic sites (loss of base)
– Approximately 100 different types of damages identified
dR
Thymine
The Chemistry of Nitric OxideDictates its Physiological Activity
Oxidation
RNOS
Guanylate CyclaseCytochromes
C,O,N Radicals(Lipid Radicals)
O2 or O2-
Direct
Indirect
L-ArginineeNOSnNOSiNOS
NO
Nitrosation DNA Strand BreaksLipid Peroxidation
HydroxylationNitrosothiolsNitrosamines
NitrotyrosineNitroguanosine
Nitration
Metal Complexes/Alkyl Radicals
Nitrosamine-Mediated Alkylation of DNA Bases
Hydroxylation
N-Nitrosodimethylamine
O6Methylguanine Guanine
CH3N2+
+
CH2O + H2O
HN
N N
N
OCH3
H2N
N N
O
H3C
H3CN N
O
H2C
H3C
O H
HN
N N
N
O
H2N
P450
ArNH2 + N2O3 ArNHNO
ArNHNO + H+ ArN2+
+ H2O
ArN2+
+ H2O ArOH + N2 +H+
Nitrosative Deamination of DNA Bases by NO-Derived N2O3
ArNH2 represents DNA bases containing an exocyclic amino group: Cytosine, methylCytosine, Guanine or Adenine
Deamination of bases
BASE DEAMINATION PRODUCT
PAIRING AFTER
REPLICATION
MUTATION
C Uracil A G:C A:T
A Hypoxanthine C A:T G:C
G Xanthine No stable pair Block to replication
5MeC Thymine A G:C A:T
Biological Consequences of DNA Damage
• Block to DNA replication– e.g. thymine glycol, abasic site
• Mutagenesis– e.g. 8-oxoguanine pairs with A as well as C
Guanine
dR
• Deletions– Common with ionizing radiation– Due to strand breakage
• Chromosomal aberrations– Double strand breaks on different chromosomes
or chromatids
• Aberrant transcription– Breakage or abasic sites believed to result in
reduced transcription– Gaps in DNA result in deleted transcripts– Consequences are altered/ mutated proteins
Types of Repair
• Mismatch Repair– Repairs mismatches, these can be generated by replication
• Nucleotide excision repair– Repairs bulky lesions predominantly, also some small
oxidative lesions• Base excision repair
– Repairs small lesions e.g. oxidative damage and deaminations
• Non-homologous end-joining– Repairs double-strand breaks in all phases of the cell cycle
• Homologous recombination– Repairs double strand breaks in the S or early G2 phases of
the cell cycle
Summary
What activates the “alarm” signals after DNA damage
• Repair proteins that initiate the different pathways recognize lesions specifically.
• Believed to be constantly “patrolling” the DNA for damage, since damage is constantly occurring.
• If repair cannot handle the damage then the cell cycle checkpoints and possibly apoptosis are activated.
• Exception maybe the generation of a DSB where signaling is rapid. Activation may occur at a similar time as repair.
Initiation of signaling
• ATM and ATR are members of the PI-3-kinase-like family of kinases.• Much of the signaling is through protein phosphorylation
ROS, RNI
e.g. BER
Sustained ssDNA
RPA
Cell cycle checkpoint
Jeggo & LobrichRadiation Protection Dosimetry2007
Activation of ATR
ROS, RNI
Cell cycle checkpoint
Occurs in S phase due to replication blockOr when there is excessive ssDNA
Jeggo & LobrichRadiation Protection Dosimetry2007
ATR signaling due to RPA bound to ssDNA caused by stalled replication or blocking lesion
• MCM2-7– Replicative DNA helicase,
unwinds the DNA
• Cdc45– Essential for initiation and
elongation of DNA synthesis
• Pol , and – DNA polymerases
• PCNA– Proliferating cell nuclear
antigen
• RPA– Replication protein A, binds
to ssDNA Not generate ssDNA
DNA Repair 6, 953
RPA on SSDNA
ATR + ATRIP (P by ATR, essential for activity)
P
Rad9-Hus1-Rad1(Binds to TopBP1,
Required for activationof ATR kinase)
Rad17 (P by ATR, aids loading 911
binds to claspin)
Claspin(P by ATR
Needs Rad17)
Assembly on ssDNA
P
TopBP1(9-1-1 loads TopBP1
+ activates ATR)
P
After loading, Chk1 that is associated with the chromatin is phosphorylated
ATR + ATRIPP
Rad9-Hus1-Rad1
Rad17
P
TopBP1
Chk1P
• Claspin channels ATR to phosphorylate Chk1
• TopB1 assists ATR-ATRIP in phosphorylating numerous substrates including Chk1
ClaspinPP
ATR phosphorylates Chk1 to stop progression to mitosis
• DNA damage causes blockage of cell cycle
Chk1
Chk1
Chk1Chk1
Chk1
Chk1
Chk1 Chk1
Chk1
Chk1Chk1
Chk1
Progression S→M
Cdc25phosphorylase
P
cytoplasm
Wee1kinase
P
Adapted from Current Biology 16, 150
Results of Activation of ATR and Chk1DNA Repair 6, 953
Summary S phase damageDNA Repair 6, 953
Most DSBs are repaired by homologous recombination in S phase
Mre11/Rad50/Nbs1
RPA binding
Mutation Research 614, 95
Activation of ATM and DSB repair
ROS, RNI
Occurs when there is a double strand breakCan be cross-talk between the two kinases ATM and ATR
Jeggo & LobrichRadiation Protection Dosimetry2007
End-bindingand synapsis
Terminal processing
Ligation
Mammaliancells
Ku70, Ku80DNA PKcs
PNK 3’ P’aseArtemis
Fen1WRN, BLM
BRCA1Pol (Pol)
Prim1 (Pol complex)
DNA Ligase IVXRCC4
Adapted from Wilson et al 2003TIBS 28,62.
Damage/ repair foci• Occurs if the protein is retained at the site of damage• Can be produced with ionizing radiation either
targeted to the nucleus or by irradiating the whole cell• Can also be produced with a laser• After irradiation cells are fixed and
immunohistochemistry used to detect proteins• Or can use fluorescent tagged proteins and in the case
of the laser the proteins can be watched in real time as they move in the nucleus and redistribute from a diffuse appearance to high intensity foci
• Has been used to determine the order of proteins moving to the DNA
NHEJ proteins form foci only if there is a lot of damage
• Not possible to see Ku proteins well even under these conditions• Likely this is due to the fast on and off movement of the proteins• Note DNA-PKcs is visible within 10 seconds and only when Ku is present in
the cell
YFP-DNA-PKCs
Irradiation site
Pre 10” 60” 180”
YFP-DNA-PKCs
Pre 10” 60” 180”
Irradiation site
Cells contain Ku
Cells do notcontain Ku
Data from David Chen, UT Southwestern
ATM activation and NHEJ likely occur at the same time
• ATM is activated quickly and is found in foci• But the proteins involved in NHEJ are also activated
rapidly but not retained at the damage unless it is severe.
• Site of a DSB is marked by a chromatin modification called gamma H2AX
• H2AX is a variant of Histone 2A and it is phosphorylated and binds to the DNA near a DSB and spreads along the DNA up to a megabase pair flanking the break site
• Believed the resolution of the foci indicates repair
Activation of ATM
• ATM is a PI-3 kinase that phosphorylates proteins• Loss of this protein results in radiosensitization• It is required to block the cell cycle in G1, S and G2• Exists as an inactive dimer, chromatin changes believed
to cause activation and it autophosphorylates
Nature 421, 499
ATM activation does not require binding to a DSB
• Phosphorylation is detectable as soon as cells can be collected after irradiation and is maximal in 5 minutes after 0.5 Gy (~50% of protein is active)
• At 0.5 Gy there are only about 18 DSBs in the genome of the cell
• Can also be induced by a few restriction site cuts• Can be activated by hypotonic swelling of cells• Can be activated by chemicals known to alter
chromatin modifications and packaging e.g. trichostatin A
• Induction of breaks thought to cause relaxation of DNA structure and this is sensed by ATM
• ATM can also be activated by:– Retinoic acid (not
cause DNA damage)– MNNG when DNA
is not present– 15-deoxy-
delta(12,14)-prostaglandin J(2), which modifies SH groups
– REDOX activation?
Cold Spring Harbor Symposia on Quantitative Biology, vol LXX, 99-109Kitagawa & Kastan
Exo/endonucleaseNeeded for ATM
at DSB
Structural maintenance of chromosome family protein
Involved in blocking cell cycle in S phase
Breast cancer associated protein
1
1
2
3
Summary of signaling
• Phosphorylated ATM is needed for gamma H2AX modification. DNA PK from NHEJ may also do the phosphorylation
• Gamma H2AX required for repair foci formation
J. Cell Biol. 173,195
-53BP1 and MDC1 are mediators of ATM signaling
-They move to the DNA and are phosphorylated by ATM
-May be docking proteins for other signaling proteins
-No known activity associated but are required for ATM signaling
-BRCA1, MDC1 and 53BP1 needed for efficient autophosphorylation of ATM
Summary of proteins involved in signaling that are retained at damage
ATM signaling
ATR andHR
NHEJ
Checkpoint signaling
ATM signaling results in blockage in G1, intra S and G2/M
p53
Smc1Chk1+Chk2
Chk1Chk2
G1 block by p53
Cyclin A and E associates with Cyclin dependent kinase 2
G1 to S progression
p21
Chk2
Chk1 and Chk2
Chk1 and 2
Phosphorylation of Cdc25A (inactivates phosphatase)
↓ Cdk2-cyclin E
Prevents Cdc45 binding to origins of replication
Blocks replication and S phase
Chk2 also alters G2/MATM
MDC1
Chk2
↓ Cdc25 phosphorylase
↑ Phosphorylated Cdc2/cyclinB
Unable to progress to mitosis
Chk1
Summary of signaling
Reactive nitrogen intermediates result in stabilization of p53
Ref1 found to influence the transcriptional activity of p53
• Loss of Ref1 resulted in reduced induction of p21 and BAX
• Involved in transcriptional and hence p53 pro-apoptotic actions
ATM implicated in redox control in cells• ATM was found due to a human disease
– Ataxia Telangiectasia
• 1 per 40,000 live births, autosomal recessive• Cerebellar ataxia- staggering gait, severe muscular
uncoordination, progressive mental retardation• Ataxia – blood vessel dilation in the eyes• Increased cancer incidence• Defective immune system • Knockout mice have higher levels of oxidative stress,
found higher H2O2, without increase in catalase• Believe cells of CNS die due to this enhanced stress• Mechanism for ATM to control oxidative stress in cells is
not known
ATM also implicated in insulin response
• AT patients show glucose intolerance and insulin-resistance
• Insulin stimulation of cells seen to activate ATM and to release elF-4E allowing increased translation of specific transcripts
• ATM in vitro found to phosphorylate elF-4E binding protein 1
• ATM knock-out mice show delayed insulin secretion when posed with a glucose challenge
• Hence ATM maybe involved in insulin signaling• and metabolic function• Altering of metabolic function could be a cause of the
enhanced oxidative stress in the cells.
Bystander effect• Irradiation of one cell, triggers stress signals in
neighboring cells that were not hit by the radiation• Do not need to damage the DNA of the irradiated
cell• The bystander cells do get chromosomal
aberrations, mutation and it can cause transformation and cell death.
• Bystander cells may have DNA damage as signaling pathways are triggered as if DSB induction has occurred.
• Cytoplasmic irradiation and mitochondria as well as ROS and RNI have been implicated.
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