Avoidance of APOBEC3B-induced mutation by error-free lesion bypass

Area of Science:

• Genetics
• Molecular Biology
• Cancer Genomics

Background:

• APOBEC cytidine deaminases are key drivers of cancer genome mutations by converting cytidines to uridines in single-stranded DNA (ssDNA).
• Uracil DNA glycosylases initiate repair, but the role of subsequent base excision repair (BER) steps on replication-associated ssDNA remains unclear.

Purpose of the Study:

• To investigate the functional role of BER and DNA damage tolerance pathways in mitigating APOBEC-induced mutations on replication-associated ssDNA.
• To elucidate the mechanisms by which cells prevent APOBEC-driven genomic alterations.

Main Methods:

• Utilized a yeast model system (CAN1 forward mutation assay) to measure APOBEC3B-induced mutation frequencies.
• Assessed mutation rates in yeast strains deficient in specific BER endonucleases (Apn1, Apn2, Ntg1, Ntg2) and DNA damage tolerance proteins (Rev3, Ubc13, Mms2, Mph1).
• Examined the impact of these deficiencies on APOBEC3B-induced canavanine resistance (CanR).

Main Results:

• Strains lacking BER endonucleases or Rev3 showed wild-type APOBEC3B-induced mutation frequencies.
• Deficiencies in error-free lesion bypass proteins Ubc13, Mms2, and Mph1 led to significant increases in APOBEC3B-induced CanR (4.9-, 2.8-, and 7.8-fold, respectively).
• This error-free bypass mechanism involving deoxyuridine conversion to abasic sites and subsequent bypass was also observed during telomere re-synthesis, albeit with reduced Ubc13 dependence.

Conclusions:

• APOBEC-induced mutations are effectively managed by deoxyuridine conversion to abasic sites and subsequent error-free bypass, particularly via template switching during DNA replication.
• A novel role for Ubc13 in regulating translesion synthesis polymerase Rev1 activity was uncovered.
• The observed APOBEC mutation signature in cancer may underestimate the full extent of genomic damage induced by these enzymes.