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Partial restoration of UV-mutagenesis P-034 in a deletion ... · UV irradiation. Survival curve...
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Partial restoration of UV-mutagenesis Partial restoration of UV-mutagenesis in a in a umuDC- umuDC- deletion mutant of deletion mutant of Escherichia Escherichia coli coli with human DNA polymerase with human DNA polymerase η η Abstract Results & Discussion References Conclusions Petr Gr Petr Gr ú ú z z *) *) and Takehiko Nohmi and Takehiko Nohmi *, *, † † ) ) ( ( * * Division of Genetics and Mutagenesis, NIHS, Tokyo; Division of Genetics and Mutagenesis, NIHS, Tokyo; † † NIBIO, Osaka) NIBIO, Osaka) NIHS DNA polymerase η (hPolη) is a key protein in translesion DNA synthesis (TLS) in human cells. Its primary function is the error free replication through UV-induced TT cyclobutane dimers which present a barrier to DNA synthesis by other eukaryotic replicative polymerases. hPolη defects underlie the genetic disease xeroderma pigmentosum variant (XPV) characterized by higher susceptibility to UV-light induced skin cancers due to erroneous replication of the UV adducts. However, hPolη is also a very low fidelity enzyme when copying undamaged DNA or DNA with other adducts and is actively recruited during the somatic hypermutation of the immunoglobulin genes. We demonstrate that hPolη restores partially the mutability and completely the survival of a UV non-mutable umuDC-deletion mutant of Escherichia coli after UVB irradiation. The catalytic core lacking the C-terminal part of hPolη was even more biologically active than the full size protein and its activity was further enhanced by attaching the prokaryotic β-subunit binding motif to it. The mutagenicity and survival effects were enhanced upon the induction of hPolη expression and its catalytically inactive variant was unable to promote any mutagenesis. This suggests that hPolη directly participates in the replication of damaged DNA in the prokaryotic bacteria. To demonstrate that our system can be useful in studying different variants of hPolη in vivo we have constructed 4 amino acid substitution mutants with altered geometry of the catalytic site analyzed previously biochemically and confirmed their altered abilities to promote mutagenesis and survival after UVB irradiation. This study paves a way to generate a variety of useful derivatives of hPolη in prokaryotic systems. Survival and induced arginine prototrophs in E. coli strains expressing the truncated human DNA polymerase η (YG9122) and its chimeras with the bacterial β-subunit binding motifs from the DNA polymerases IV (YG9126) and RI (YG9127) after UV irradiation. Survival curve points are labeled as squares while the mutation curve points are labeled as triangles. Dashed lines symbolize the experiments where IPTG was added to the growing cultures prior to irradiation to enhance the expression of the polymerase. The control strain harboring the empty expression vector only (YG9112) as well as the wild type strain AB1157 natively expressing its endogenous Y- family DNA polymerase PolV are shown for comparison too. The frequencies of arginine revertants induced by UV light were calculated by subtracting the spontaneous revertant counts (without any irradiation) from the experimental values. Error bars represent the standard deviations calculated from 3 plates per each dose. Schematic drawing of the human DNA polymerase η constructs used in this study. The 20 amino acid long N-terminal HisTag-leader sequence present in all proteins is shown above the full size protein (Pol η). The C-terminally truncated protein is labeled as Pol ηΔC and the amino acid sequences of the β-subunit binding motifs (clamp interacting motif) attached at its C-terminus to create the chimeras are shown above and underneath the construct labeled Polη-β with the critical amino acids of the motif in red. Polη 733 a.a. MNHKVD(H) 10 TMGHM-22 Polη-β 546 a.a. Polη∆ C 531 a.a. GGGGG QMERQLVLG L GGGGG KEAQLDLF DS PolIV type PolRI type PolηCD 733 a.a. 127-VIERASIAA AYVDLT-143 hinge linker clamp interacting motif The PolIV β-subunit sliding clamp in action as determined by crystallography (Bunting at al. 2003). Gruz P, Nohmi T (2013) Expression and Activity of Human DNA Polymerase η in Escherichia coli . Genes and Environment 35: 10-20 Bunting KA, Roe SM, Pearl LH (2003) Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. EMBO J 22: 5883-5892 Katafuchi A, Sassa A, Niimi N, Gruz P, Fujimoto H, Masutani C, Hanaoka F, Ohta T, Nohmi T (2010) Critical amino acids in human DNA polymerases eta and kappa involved in erroneous incorporation of oxidized nucleotides. Nucleic acids research 38: 859-867 Xie J, Litman R, Wang S, Peng M, Guillemette S, Rooney T, Cantor SB (2010) Targeting the FANCJ-BRCA1 interaction promotes a switch from recombination to poleta-dependent bypass. Oncogene 29: 2499-2508 - + - + - + - + - + - + - + - + - + - + YG9112 YG9113 YG9120 YG9121 YG9124 YG9125 YG9119 YG9122 YG9126 YG9127 Marker [kDa] 100 70 60 50 150 IPTG 80 40 30 Full-sized hPolη hPolη∆ C WT F18A S62G R61A R61K D115A E116A Empty vector WT + PolIV- type tail + PolRI- type tail Different variants of the human DNA polymerase η protein expressed in the new E. coli tester strains. The picture shows Western blot of total cell proteins separated in a 10% SDS-PAGE gel and probed with the monoclonal anti- HisTag antibodies. The presence or absence of IPTG in each culture is indicated above the lanes. 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9112 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9122 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9126 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9127 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] YG9122 (hPolη∆ C WT) YG9126 (+ PolIV-type tail) YG9127 (+ PolRI-type tail) 012 34 56 78 9 1.5 15 150 0 200 400 600 800 1000 1200 1400 1600 AB1157 YG9112 empty vector 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9119 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9120 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9124 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9125 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9113 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] 0 1 2 3 4 5 6 7 8 9 1.5 15 150 -10 40 90 140 190 240 290 340 YG9121 UV-B [kJ/m2] Survival [%] Induced Arg+ reversions [x10-8] YG9113 (WT) YG9119 (D115A, E116A) YG9120 (F18A) YG9124 (R61A) YG9125 (R61K) YG9121 (S62G) YG9124 (R61A) Survival and induced arginine prototrophs in E. coli strains expressing different mutants of the human DNA polymerase η after UV irradiation. Survival curve points are labeled as squares while the mutation curve points are labeled as triangles. Dashed lines symbolize the experiments where IPTG was added to the growing cultures prior to irradiation to enhance the expression of the polymerase. The frequencies of arginine revertants induced by UV light were calculated by subtracting the spontaneous revertant counts (without any irradiation) from the experimental values. Error bars represent the standard deviations calculated from 3 plates per each dose. Start 10xHisTag TTTTGTTTAACTTTAAGAAGGAGATATACCATGAATCACAAAGTGGATCATCATCATCATCATCATCATCATCATCACACCATG -------- ===== ================ ---------------------------------- U-Region s10 S.D. Downstream Box CA repeat S.D. Start DB NcoI Details of the translation initiation region derived from the highly efficient pYG8582 overexpression vector which has been used to drive hPolη expression in all vectors employed in this study (backbone is from the low copy number plasmid pWSK129 carrying the lac promoter). Shown is the mRNA secondary structure prediction of the translation initiation region as calculated by the program Mfold. The N-terminal 10xHisTag is a part of the translational enhancer and is displayed in blue on the picture. E. coli strain Description hPolη mutation AB1157 Wild type K-12 derivative carrying the argE3 (ochre) reversion marker YG6168 UV non-mutable derivative of AB1157 carrying the Δ(umuDC)596::ermGT disruption YG9112 YG6168 derivative harboring the empty expression vector pWSK129 YG9113 YG6168 derivative expressing human DNA polymerase η from the plasmid pYG8626 wild type YG9119 YG6168 derivative expressing catalytically dead human DNA polymerase η from the plasmid pYG8636 D115A+E116A YG9120 YG6168 derivative expressing the steric gate mutant of human DNA polymerase η from the plasmid pYG8637 F18A YG9121 YG6168 derivative expressing the superactive mutant of human DNA polymerase η from the plasmid pYG8638 S62G YG9124 YG6168 derivative expressing the Arg61->Ala61 mutant of human DNA polymerase η from the plasmid pYG8639 R61A YG9125 YG6168 derivative expressing the Arg61->Lys61 mutant of human DNA polymerase η from the plasmid pYG8640 R61K YG9122 YG6168 derivative expressing C-terminally truncated DNA polymerase η from the plasmid pYG8633 containing only its essential catalytic domain ΔC YG9126 YG6168 derivative expressing the chimerical human DNA polymerase η with the attached DinB (PolIV) β-subunit binding motif from the plasmid pYG8634 ΔC+PolIV-type tail YG9127 YG6168 derivative expressing the chimerical human DNA polymerase η with the attached MucB (PolRI) β-subunit binding motif from the plasmid pYG8635 ΔC+PolRI-type tail P-034 Human DNA polymerase η (hPolη) is the most well studied Y-family DNA polymerase responsible for the inherited disease XPV syndrome and is mechanistically involved in the initiation of cancers associated with the BRCA1 mutations. We have successfully expressed hPolη in the prokaryotic model bacterium Escherichia coli as confirmed by Western blotting and response to IPTG induction. hPolη remained functional in E. coli and participated in the translesion DNA synthesis across CPD lesions induced by UVB radiation. The activity of hPolη in E. coli was remarkably increased by removing its C-terminal part carrying motifs specific to eukaryotes and completely abolished by substituting 2 essential residues within its catalytic site. Chimeric hPolη proteins carrying the prokaryotic DNA targeting motifs showed increased ability to promote UVB mutagenesis. A single amino acid substitution within the motif II of finger domain (S62G) significantly enhanced hPolη abilities to increase survival and mutagenesis after UVB irradiation in vivo. The hPolη steric gate mutant (F18A), although biochemically active in vitro, completely lost its activity in vivo. Substitution of the amino acid residue guiding the 8oxo-dGTP misincorporation opposite template dA in vitro (R61) produced mutants of hPolη which lost the ability to promote mutagenesis at low expression level in vivo and suppressed the survival after UVB irradiation. Our new system allows for the generation and analysis of the effects of various hPolη mutations on this enzyme's functionality during TLS in enterobacteria as well as for testing the intrinsic ability of hPolη to modulate TLS across other types of DNA adducts in vivo. Enterobacterial strains used in the study
Transcript of Partial restoration of UV-mutagenesis P-034 in a deletion ... · UV irradiation. Survival curve...
Partial restoration of UV-mutagenesis Partial restoration of UV-mutagenesis in a in a umuDC-umuDC-deletion mutant ofdeletion mutant of Escherichia Escherichia
coli coli with human DNA polymerase with human DNA polymerase ηη
Abstract
Results & Discussion
References
Conclusions
Petr GrPetr Grúúzz*)*) and Takehiko Nohmi and Takehiko Nohmi*,*,††))
((**Division of Genetics and Mutagenesis, NIHS, Tokyo; Division of Genetics and Mutagenesis, NIHS, Tokyo; ††NIBIO, Osaka)NIBIO, Osaka)NIHS
DNA polymerase η (hPolη) is a key protein in translesion DNA synthesis (TLS) in human cells. Its primary function is the error free replication through UV-induced TT cyclobutane dimers which present a barrier to DNA synthesis by other eukaryotic replicative polymerases. hPolη defects underlie the genetic disease xeroderma pigmentosum variant (XPV) characterized by higher susceptibility to UV-light induced skin cancers due to erroneous replication of the UV adducts. However, hPolη is also a very low fidelity enzyme when copying undamaged DNA or DNA with other adducts and is actively recruited during the somatic hypermutation of the immunoglobulin genes.
We demonstrate that hPolη restores partially the mutability and completely the survival of a UV non-mutable umuDC-deletion mutant of Escherichia coli after UVB irradiation. The catalytic core lacking the C-terminal part of hPolη was even more biologically active than the full size protein and its activity was further enhanced by attaching the prokaryotic β-subunit binding motif to it. The mutagenicity and survival effects were enhanced upon the induction of hPolη expression and its catalytically inactive variant was unable to promote any mutagenesis. This suggests that hPolη directly participates in the replication of damaged DNA in the prokaryotic bacteria.
To demonstrate that our system can be useful in studying different variants of hPolη in vivo we have constructed 4 amino acid substitution mutants with altered geometry of the catalytic site analyzed previously biochemically and confirmed their altered abilities to promote mutagenesis and survival after UVB irradiation. This study paves a way to generate a variety of useful derivatives of hPolη in prokaryotic systems.
Survival and induced arginine prototrophs in E. coli strains expressing the truncated human DNA polymerase η (YG9122) and its chimeras with the bacterial β-subunit binding motifs from the DNA polymerases IV (YG9126) and RI (YG9127) after UV irradiation. Survival curve points are labeled as squares while the mutation curve points are labeled as triangles. Dashed lines symbolize the experiments where IPTG was added to the growing cultures prior to irradiation to enhance the expression of the polymerase. The control strain harboring the empty expression vector only (YG9112) as well as the wild type strain AB1157 natively expressing its endogenous Y-family DNA polymerase PolV are shown for comparison too. The frequencies of arginine revertants induced by UV light were calculated by subtracting the spontaneous revertant counts (without any irradiation) from the experimental values. Error bars represent the standard deviations calculated from 3 plates per each dose.
Schematic drawing of the humanDNA polymerase η constructsused in this study. The 20 amino acidlong N-terminal HisTag-leader sequencepresent in all proteins is shown above the full size protein (Polη). The C-terminally truncated protein is labeled as PolηΔC and the amino acid sequences of the β-subunit binding motifs (clamp interacting motif) attached at its C-terminus to create the chimeras are shown above and underneath the construct labeled Polη-β with the critical amino acids of the motif in red.
Polη 733 a.a.
MNHKVD(H)10TMGHM-22
Polη−β 546 a.a.
Polη∆C 531 a.a.
GGGGGQMERQLVLGL
GGGGGKEAQLDLFDS
PolIV type
PolRI type
PolηCD 733 a.a.127-VIERASIAAAYVDLT-143
hinge linker clampinteractingmotif
The PolIV β-subunit sliding clamp in action as determined by crystallography (Bunting at al. 2003).
Gruz P, Nohmi T (2013) Expression and Activity of Human DNA Polymerase η in Escherichia coli. Genes and Environment 35: 10-20
Bunting KA, Roe SM, Pearl LH (2003) Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. EMBO J 22: 5883-5892
Katafuchi A, Sassa A, Niimi N, Gruz P, Fujimoto H, Masutani C, Hanaoka F, Ohta T, Nohmi T (2010) Critical amino acids in human DNA polymerases eta and kappa involved in erroneous incorporation of oxidized nucleotides. Nucleic acids research 38: 859-867
Xie J, Litman R, Wang S, Peng M, Guillemette S, Rooney T, Cantor SB (2010) Targeting the FANCJ-BRCA1 interaction promotes a switch from recombination to poleta-dependent bypass. Oncogene 29: 2499-2508
- + - + - + - + - + - + - + - + - + - +
YG
9112
YG
9113
YG
9120
YG
9121
YG
9124
YG
9125
YG
9119
YG
9122
YG
9126
YG
9127
Marker[kDa]
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150
IPTG
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Full-sized hPolη hPolη∆C
WT F18A S62G R61A R61KD115AE116A
Emptyvector WT
+ PolIV-type tail
+ PolRI-type tail
Different variants of the human DNA polymerase η protein expressed in the new E. coli tester strains. The picture shows Western blot of total cell proteins separated in a 10% SDS-PAGE gel and probed with the monoclonal anti-HisTag antibodies. The presence or absence of IPTG in each culture is indicated above the lanes.
0 1 2 3 4 5 6 7 8 91.5
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150
-10
40
90
140
190
240
290
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YG9112
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
uce
d A
rg+
re
vers
ion
s [x
10
-8]
0 1 2 3 4 5 6 7 8 91.5
15
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-10
40
90
140
190
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290
340
YG9122
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
uce
d A
rg+
re
vers
ion
s [x
10
-8]
0 1 2 3 4 5 6 7 8 91.5
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150
-10
40
90
140
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240
290
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YG9126
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
uce
d A
rg+
re
vers
ion
s [x
10
-8]
0 1 2 3 4 5 6 7 8 91.5
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YG9127
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
uce
d A
rg+
re
vers
ion
s [x
10
-8]
YG9122 (hPolη∆C WT)YG9126 (+ PolIV-type tail) YG9127 (+ PolRI-type tail)
0 1 2 3 4 5 6 7 8 91.5
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150
0
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AB1157
YG9112empty vector
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YG9119
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
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d A
rg+
re
vers
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s [x
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0 1 2 3 4 5 6 7 8 91.5
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YG9120
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
uce
d A
rg+
re
vers
ion
s [x
10
-8]
0 1 2 3 4 5 6 7 8 91.5
15
150
-10
40
90
140
190
240
290
340
YG9124
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
uce
d A
rg+
re
vers
ion
s [x
10
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0 1 2 3 4 5 6 7 8 91.5
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150
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90
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190
240
290
340
YG9125
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
uce
d A
rg+
re
vers
ion
s [x
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-8]
0 1 2 3 4 5 6 7 8 91.5
15
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140
190
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290
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YG9113
UV-B [kJ/m2]
Sur
viva
l [%
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Ind
uce
d A
rg+
re
vers
ion
s [x
10
-8]
0 1 2 3 4 5 6 7 8 91.5
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150
-10
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90
140
190
240
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YG9121
UV-B [kJ/m2]
Sur
viva
l [%
]
Ind
uce
d A
rg+
re
vers
ion
s [x
10
-8]
YG9113 (WT) YG9119 (D115A, E116A) YG9120 (F18A)
YG9124 (R61A)YG9125 (R61K) YG9121 (S62G)YG9124 (R61A)
Survival and induced arginine prototrophs in E. coli strains expressing different mutants of the human DNA polymerase η after UV irradiation. Survival curve points are labeled as squares while the mutation curve points are labeled as triangles. Dashed lines symbolize the experiments where IPTG was added to the growing cultures prior to irradiation to enhance the expression of the polymerase. The frequencies of arginine revertants induced by UV light were calculated by subtracting the spontaneous revertant counts (without any irradiation) from the experimental values. Error bars represent the standard deviations calculated from 3 plates per each dose.
Start 10xHisTagTTTTGTTTAACTTTAAGAAGGAGATATACCATGAATCACAAAGTGGATCATCATCATCATCATCATCATCATCATCACACCATG-------- ===== ================ ----------------------------------
URegion s10 S.D. Downstream Box CA repeat
S.D. Start
DB
NcoI
Details of the translation initiation region derived from the highly efficient pYG8582 overexpression vector which has been used to drive hPolη expression in all vectors employed in this study (backbone is from the low copy number plasmid pWSK129 carrying the lac promoter). Shown is the mRNA secondary structure prediction of the translation initiation region as calculated by the program Mfold. The N-terminal 10xHisTag is a part of the translational enhancer and is displayed in blue on the picture.
E. coli strain Description hPolη mutation
AB1157 Wild type K-12 derivative carrying the argE3 (ochre) reversion marker
YG6168 UV non-mutable derivative of AB1157 carrying the Δ(umuDC)596::ermGT disruption
YG9112 YG6168 derivative harboring the empty expression vector pWSK129
YG9113YG6168 derivative expressing human DNA polymerase η from the plasmid pYG8626 wild type
YG9119 YG6168 derivative expressing catalytically dead human DNA polymerase η from the plasmid pYG8636
D115A+E116A
YG9120YG6168 derivative expressing the steric gate mutant of human DNA polymerase η from the plasmid pYG8637 F18A
YG9121YG6168 derivative expressing the superactive mutant of human DNA polymerase η from the plasmid pYG8638 S62G
YG9124 YG6168 derivative expressing the Arg61->Ala61 mutant of human DNA polymerase η from the plasmid pYG8639
R61A
YG9125YG6168 derivative expressing the Arg61->Lys61 mutant of human DNA polymerase η from the plasmid pYG8640 R61K
YG9122YG6168 derivative expressing C-terminally truncated DNA polymerase η from the plasmid pYG8633 containing only its essential catalytic domain ΔC
YG9126YG6168 derivative expressing the chimerical human DNA polymerase η with the attached DinB (PolIV) β-subunit binding motif from the plasmid pYG8634
ΔC+PolIV-type tail
YG9127YG6168 derivative expressing the chimerical human DNA polymerase η with the attached MucB (PolRI) β-subunit binding motif from the plasmid pYG8635
ΔC+PolRI-type tail
P-034
Human DNA polymerase η (hPolη) is the most well studied Y-family DNA polymerase responsible for the inherited disease XPV syndrome and is mechanistically involved in the initiation of cancers associated with the BRCA1 mutations.
We have successfully expressed hPolη in the prokaryotic model bacterium Escherichia coli as confirmed by Western blotting and response to IPTG induction.
hPolη remained functional in E. coli and participated in the translesion DNA synthesis across CPD lesions induced by UVB radiation.
The activity of hPolη in E. coli was remarkably increased by removing its C-terminal part carrying motifs specific to eukaryotes and completely abolished by substituting 2 essential residues within its catalytic site.
Chimeric hPolη proteins carrying the prokaryotic DNA targeting motifs showed increased ability to promote UVB mutagenesis.
A single amino acid substitution within the motif II of finger domain (S62G) significantly enhanced hPolη abilities to increase survival and mutagenesis after UVB irradiation in vivo.
The hPolη steric gate mutant (F18A), although biochemically active in vitro, completely lost its activity in vivo.
Substitution of the amino acid residue guiding the 8oxo-dGTP misincorporation opposite template dA in vitro (R61) produced mutants of hPolη which lost the ability to promote mutagenesis at low expression level in vivo and suppressed the survival after UVB irradiation.
Our new system allows for the generation and analysis of the effects of various hPolη mutations on this enzyme's functionality during TLS in enterobacteria as well as for testing the intrinsic ability of hPolη to modulate TLS across other types of DNA adducts in vivo.
Enterobacterial strains used in the study
