The Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression

Abstract

DNA damage must be repaired in an accurate and timely fashion to preserve genome stability. Cellular mechanisms preventing genome instability are crucial to human health because genome instability is considered a hallmark of cancer. Collectively referred to as the DNA damage response, conserved pathways ensure proper DNA damage recognition and repair. The function of numerous DNA damage response components is fine-tuned by posttranslational modifications, including ubiquitination. This not only involves the enzyme cascade responsible for conjugating ubiquitin to substrates but also requires enzymes that mediate directed removal of ubiquitin. Deubiquitinases remove ubiquitin from substrates to prevent degradation or to mediate signaling functions. The Saccharomyces cerevisiae deubiquitinase Ubp7 has been characterized previously as an endocytic factor. However, here we identify Ubp7 as a novel factor affecting S phase progression after hydroxyurea treatment and demonstrate an evolutionary and genetic interaction of Ubp7 with DNA damage repair pathways of homologous recombination and nucleotide excision repair. We find that deletion of UBP7 sensitizes cells to hydroxyurea and cisplatin and demonstrate that factors that stabilize replication forks are critical under these conditions. Furthermore, ubp7⌬ cells exhibit an S phase progression defect upon checkpoint activation by hydroxyurea treatment. ubp7⌬ mutants are epistatic to factors involved in histone maintenance and modification, and we find that a subset of Ubp7 is chromatin-associated. In summary, our results suggest that Ubp7 contributes to S phase progression by affecting the chromatin state at replication forks, and we propose histone H2B ubiquitination as a potential substrate of Ubp7.

Evolution-based screening enables genome-wide prioritization and discovery of DNA repair genes

“…Genes involved in the same biological process often exhibit elevated ERC with each other, comprising a statistically coevolving group (3,4). Querying additional genes for correlation with these groups has proven effective in uncovering novel roles for genes in previously unrelated processes in model organisms such as worms, flies, and yeast (4)(5)(6). More broadly, ERC may be investigated between processes, revealing novel interdependencies at the systems level, and can be expanded to analyze crosstalk between networks (7).…”

Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer

“…FACS samples were pelleted and washed once with water before being fixed with 70% EtOH and stored in the dark at 4ºC. Subsequently, the samples were treated with protease and RNase and DNA was stained with propidium iodide and analyzed by FACS as described (54).…”

Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations

“…The approach has been used to detect physical interactions within and among proteins, as well as shared functionality not involving physical interaction, such as within metabolic pathways (Clark, Alani & Aquadro, 2012). For example, it has been employed to identify gene networks for post-mating response (Findlay et al, 2014), ubiquitination (Böhm et al, 2016), and recombination (Godin et al, 2015), and more recently to identify DNA repair genes (Brunette et al, 2019), cadherin-associated proteins (Raza et al, 2019), mitochondrial-nuclear interactions (Yan, Ye & Werren, 2019), and a mitochondrial associated zinc transporter (Kowalczyk et al, 2021), with subsequent experimental support. Evolutionary rate correlation (ERC) approaches are relatively inexpensive screening tools for detecting candidate protein interactions, and can also detect novel protein interactions that are not readily found in more traditional proteomic and genetic approaches (Colgren & Nichols, 2019;Yan, Ye & Werren, 2019).…”