Architecturally diverse proteins converge on an analogous mechanism to inactivate Uracil-DNA glycosylase

Abstract

Uracil-DNA glycosylase (UDG) compromises the replication strategies of diverse viruses from unrelated lineages. Virally encoded proteins therefore exist to limit, inhibit or target UDG activity for proteolysis. Viral proteins targeting UDG, such as the bacteriophage proteins ugi, and p56, and the HIV-1 protein Vpr, share no sequence similarity, and are not structurally homologous. Such diversity has hindered identification of known or expected UDG-inhibitory activities in other genomes. The structural basis for UDG inhibition by ugi is well characterized; yet, paradoxically, the structure of the unbound p56 protein is enigmatically unrevealing of its mechanism. To resolve this conundrum, we determined the structure of a p56 dimer bound to UDG. A helix from one of the subunits of p56 occupies the UDG DNA-binding cleft, whereas the dimer interface forms a hydrophobic box to trap a mechanistically important UDG residue. Surprisingly, these p56 inhibitory elements are unexpectedly analogous to features used by ugi despite profound architectural disparity. Contacts from B-DNA to UDG are mimicked by residues of the p56 helix, echoing the role of ugi’s inhibitory beta strand. Using mutagenesis, we propose that DNA mimicry by p56 is a targeting and specificity mechanism supporting tight inhibition via hydrophobic sequestration.

Structural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones

“…However, inhibition of SbcCD is unlikely to contribute to the antibacterial potentiation effect observed here, because cells lacking SbcCD activity are not sensitive to ciprofloxacin (Henderson and Kreuzer, 2015; Aedo and Tse-Dinh, 2013; Liu et al, 2010). DNA mimicry has been observed previously for phage-encoded proteins that target type I restriction endonucleases and glycosylases (Kennaway et al, 2009; Baños-Sanz et al, 2013; Cole et al, 2013) and it may be a common mechanism for bacteriophages to modulate DNA replication and repair in their hosts. Bacteriophage P22 codes for another, distinctive RecBCD inhibitor called Abc2 but this operates by a poorly-characterised mechanism (Murphy, 2000).…”

Life without dUTPase

“…In these phages, they either enable synthesis of uracil-enriched DNA or protect against the cleavage of phage genome at uracil positions thereby facilitating viral DNA replication (Cole et al, 2013). Uracilation of viral DNA also plays a role in other host-virus interactions (Chen et al, 2002; Sire et al, 2008).…”

“…The very first finding that led to the identification of UGI was that Bacillus subtilis bacteriophages PBS1, and PBS2 possess a genome in which thymine is replaced by uracil (Takahashi and Marmur, 1963). UGI is an early phage protein that prevents degradation by the host UNG and therefore it is indispensable for the maintenance of the uracilated phage genome (Cone et al, 1980; Cole et al, 2013). To date two other bacteriophages have been discovered that possess uracil containing DNA, namely, ΦR1-37 infecting Y. enterocolitica (Kiljunen et al, 2005), and phage S6 infecting Staphylococcace (Uchiyama et al, 2014).…”

The Essential Co-Option of Uracil-DNA Glycosylases by Herpesviruses Invites Novel Antiviral Design

“…If that is not surprising enough, γ-herpesvirus Ung includes the exaptation of a key motif essential for Ung catalysis to underpin viral replication competence ( Figure 5) [49][50][51][52]. The aforementioned Ung catalytic motif is, in fact, the same one that, in the host Ung and its canonical relatives in bacteria, is targeted by viruses that silence the cellular Ung protein as part of their replication strategy ( Figure 5) [70][71][72].…”

“…Intriguingly this conserved mechanism has evolved convergently from three independent, unrelated protein architectures: Ugi [and its structural homologue SAUGI, a horizontally transferred gene found in SCCmec mobile genetic elements of Staphylococcaceae] from myoviruses, p56 from salasviruses and Vpr from primate lentiviruses. Charge-based alignment and contact from the inhibitor protein elicits concerted Ung loop motion, resulting in an effectively irreversible sterically-blockaded sequestration of Ung via hydrophobic trapping of the apical aliphatic side chain of the Ung loop by the virus inhibitor protein ( Figure 5) [41,[70][71][72]76].…”