AID, APOBEC3A and APOBEC3B efficiently deaminate deoxycytidines neighboring DNA damage induced by oxidation or alkylation

AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and Y...

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Published inBiochimica et biophysica acta. General subjects Vol. 1863; no. 11; p. 129415
Main Authors Diamond, Cody P., Im, Junbum, Button, Erynn A., Huebert, David N.G., King, Justin J., Borzooee, Faeze, Abdouni, Hala S., Bacque, Lisa, McCarthy, Erin, Fifield, Heather, Berghuis, Lesley M., Larijani, Mani
Format Journal Article
LanguageEnglish
Published Netherlands Elsevier B.V 01.11.2019
Subjects
AID/APOBEC
alkylation
Cancer
catalytic activity
Cytidine Deaminase - chemistry
Cytidine Deaminase - metabolism
Deaminases
Deamination
deoxycytidine
Deoxycytidine - chemistry
Deoxycytidine - metabolism
DNA
DNA Damage
drug therapy
enzymes
genomics
Humans
immunity
Minor Histocompatibility Antigens - chemistry
Minor Histocompatibility Antigens - metabolism
Mutation
neoplasms
nucleotide motifs
nucleotides
oxidation
Oxidation-Reduction
Proteins - chemistry
Proteins - metabolism
Sequence specificity
Deaminases
Sequence specificity
Mutation
AID/APOBEC
DNA damage
Cancer
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Abstract AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases. Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs. All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases. AID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged. Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered. •AID, APOBEC3A and APOBEC3B can act on certain damaged DNA sequences more efficiently than their most favored normal hotspots•AID, APOBEC3A and APOBEC3B can recognize and act on DNA that is damaged by environmental or chemotherapeutic agents•The DNA binding motifs on the surfaces of AID, APOBEC3A and APOBEC3B recognize specific damaged bases
AbstractList AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases. Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs. All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases. AID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged. Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered.
AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases. Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs. All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases. AID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged. Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered. •AID, APOBEC3A and APOBEC3B can act on certain damaged DNA sequences more efficiently than their most favored normal hotspots•AID, APOBEC3A and APOBEC3B can recognize and act on DNA that is damaged by environmental or chemotherapeutic agents•The DNA binding motifs on the surfaces of AID, APOBEC3A and APOBEC3B recognize specific damaged bases
AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases.Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs.All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases.AID, A3A and A3B efficiently recognize and deaminate dC whose surrounding nucleotides are damaged.Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered.
AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases.BACKGROUNDAID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases.Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs.METHODSSubstrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs.All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases.RESULTSAll three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases.AID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged.CONCLUSIONSAID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged.Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered.GENERAL SIGNIFICANCEBeyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered.
ArticleNumber 129415
Author Im, Junbum
King, Justin J.
Fifield, Heather
Borzooee, Faeze
Bacque, Lisa
Berghuis, Lesley M.
Abdouni, Hala S.
Larijani, Mani
Button, Erynn A.
Diamond, Cody P.
Huebert, David N.G.
McCarthy, Erin
Author_xml – sequence: 1
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  surname: Diamond
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  givenname: Junbum
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  organization: Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3V6, Canada
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  surname: Borzooee
  fullname: Borzooee, Faeze
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  givenname: Hala S.
  surname: Abdouni
  fullname: Abdouni, Hala S.
  organization: Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3V6, Canada
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  givenname: Lisa
  surname: Bacque
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  organization: Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3V6, Canada
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  givenname: Erin
  surname: McCarthy
  fullname: McCarthy, Erin
  organization: Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3V6, Canada
– sequence: 10
  givenname: Heather
  surname: Fifield
  fullname: Fifield, Heather
  organization: Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3V6, Canada
– sequence: 11
  givenname: Lesley M.
  surname: Berghuis
  fullname: Berghuis, Lesley M.
  organization: Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3V6, Canada
– sequence: 12
  givenname: Mani
  surname: Larijani
  fullname: Larijani, Mani
  email: mani_larijani@sfu.ca
  organization: Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3V6, Canada
BackLink https://www.ncbi.nlm.nih.gov/pubmed/31404619$$D View this record in MEDLINE/PubMed
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ISSN 0304-4165
1872-8006
IngestDate Fri Jul 11 01:03:58 EDT 2025
Fri Jul 11 16:51:33 EDT 2025
Wed Feb 19 02:30:49 EST 2025
Thu Apr 24 23:11:42 EDT 2025
Tue Jul 01 00:22:12 EDT 2025
Fri Feb 23 02:34:14 EST 2024
IsPeerReviewed true
IsScholarly true
Issue 11
Keywords Deaminases
Sequence specificity
Mutation
AID/APOBEC
DNA damage
Cancer
Language English
License Copyright © 2019 Elsevier B.V. All rights reserved.
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PublicationTitle Biochimica et biophysica acta. General subjects
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Snippet AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to...
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SubjectTerms AID/APOBEC
alkylation
Cancer
catalytic activity
Cytidine Deaminase - chemistry
Cytidine Deaminase - metabolism
Deaminases
Deamination
deoxycytidine
Deoxycytidine - chemistry
Deoxycytidine - metabolism
DNA
DNA Damage
drug therapy
enzymes
genomics
Humans
immunity
Minor Histocompatibility Antigens - chemistry
Minor Histocompatibility Antigens - metabolism
Mutation
neoplasms
nucleotide motifs
nucleotides
oxidation
Oxidation-Reduction
Proteins - chemistry
Proteins - metabolism
Sequence specificity
Title AID, APOBEC3A and APOBEC3B efficiently deaminate deoxycytidines neighboring DNA damage induced by oxidation or alkylation
URI https://dx.doi.org/10.1016/j.bbagen.2019.129415
https://www.ncbi.nlm.nih.gov/pubmed/31404619
https://www.proquest.com/docview/2272736796
https://www.proquest.com/docview/2388785628
Volume 1863
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