Yeast HMGB protein Hmo1 is a multifaceted regulator of DNA damage tolerance

Abstract

The chromosome architecture protein Hmo1 in Saccharomyces cerevisiae is categorized as an HMGB protein as it consists of two structure-specific DNA binding HMGB motifs. However, it deviates from canonical HMGB proteins that have acidic C-terminal domains (CTDs) by bearing a basic one. Hmo1 plays diverse functions in gene regulation and genome integrity. There is evidence implicating Hmo1 in DNA damage tolerance (DDT) that enables DNA replication to bypass lesions on the template. Hmo1 is believed to direct DNA lesions to the error-free template switching (TS) pathway of DDT and aids in the formation of the key TS intermediate sister chromatid junction (SCJ), but the underlying mechanism(s) has yet to be resolved. In this work, we took genetics and molecular biology approaches to further investigate the role of Hmo1 in DDT. We found extensive functional interactions of Hmo1 with components of the genome integrity network in cellular response to the genotoxin methyl methanesulfonate (MMS), implicating Hmo1 in multiple processes in the execution or regulation of homology-directed DNA repair, replication-coupled chromatin assembly, and cell cycle checkpoint. Notably, our data pointed to a role of Hmo1 in directing SJC to the nuclease-mediated resolution pathway instead of the helicase/topoisomerase mediated dissolution pathway for processing/removal. They also suggested that Hmo1 modulates both the recycling of parental histones and the deposition of newly synthesized histones at the replication fork to ensure proper chromatin formation on nascent DNA that is important for DDT. We found evidence that Hmo1 antagonizes the function of histone H2A variant H2A.Z (also known as Htz1 in yeast) in DDT. We also found that Hmo1 is required for DNA damage checkpoint signaling induced by MMS as wells as for DNA negative supercoiling as a proxy of chromatin structure. Moreover, we obtained evidence indicating that the CTD of Hmo1 may or may not be required for its function in DDT depending on the genetic background of the host. Taken together, our findings demonstrate that Hmo1 can contribute to, or regulate, multiple processes of DDT via different mechanisms.