Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD

Abstract

The Escherichia coli SOS response, an induced DNA damage response pathway, confers survival on bacterial cells by providing accurate repair mechanisms as well as the potentially mutagenic pathway translesion synthesis (TLS). The umuD gene products are upregulated after DNA damage and play roles in both nonmutagenic and mutagenic aspects of the SOS response. Full-length UmuD is expressed as a homodimer of 139-amino-acid subunits, which eventually cleaves its N-terminal 24 amino acids to form UmuD'. The cleavage product UmuD' and UmuC form the Y-family polymerase DNA Pol V (UmuD'C) capable of performing TLS. UmuD and UmuD' exist as homodimers, but their subunits can readily exchange to form UmuDD' heterodimers preferentially. Heterodimer formation is an essential step in the degradation pathway of UmuD'. The recognition sequence for ClpXP protease is located within the first 24 amino acids of full-length UmuD, and the partner of full-length UmuD, whether UmuD or UmuD', is degraded by ClpXP. To better understand the mechanism by which UmuD subunits exchange, we measured the kinetics of exchange of a number of fluorescently labeled single-cysteine UmuD variants as detected by Förster resonance energy transfer. Labeling sites near the dimer interface correlate with increased rates of exchange, indicating that weakening the dimer interface facilitates exchange, whereas labeling sites on the exterior decrease the rate of exchange. In most but not all cases, homodimer and heterodimer exchange exhibit similar rates, indicating that somewhat different molecular surfaces mediate homodimer exchange and heterodimer formation.

The SOS system: A complex and tightly regulated response to DNA damage

“…UmuD and UmuD′ exist as homodimers, but their subunits can readily exchange to form UmuDD′ heterodimers preferentially. Murison et al () measured the kinetics of exchange of a number of fluorescently labeled single‐cysteine UmuD variants and demonstrated that somewhat different molecular surfaces mediate homodimer exchange and heterodimer formation. Importantly, in the heterodimer context, UmuD′ is specifically degraded by the ClpXP protease (Frank et al, ).…”

Betulinic Acid Prevents the Acquisition of Ciprofloxacin-Mediated Mutagenesis in Staphylococcus aureus

“…After this, the expression of SOS-related genes is activated, resulting in the inhibition of the cell division process, in order to repair the DNA [13,18]. However, when the integrity of both DNA strands is affected, the expression of error-prone DNA polymerases is activated and their low fidelity might result in bacterial mutagenesis [19,20,21].…”

Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments

“…In response to DNA damage (e.g., caused by UV radiation), umuCD -encoded DNA polymerase of the Y family, enables DNA synthesis past lesions in the template strand. Therefore, the umuCD genes play an important role in maintaining genome stability in bacteria (Goodman et al, 2016; Murison et al, 2017). Genomic analysis revealed that these DNA repair systems are often found within plasmids of cold-active bacteria, especially those originating from polar regions (Dziewit and Bartosik, 2014).…”