Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases

Liao, Yi; Lin, San‐Yih; Ko, Tzu Ping; Liu, Chang Yi; Hsu, Kai Cheng; Wang, Hao Ching

doi:10.1016/j.ijbiomac.2020.05.267

Cited by 2 publications

(2 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Inhibition of uracil DNA glycosylase also sensitizes cancer cells to 5-FdUrd similar to like dUTPase inhibition [ 35 ]. UNG is also essential for some DNA viruses that infect humans, e.g., herpesviruses, so it has been considered as a target for potential antiviral drug candidates [ 36 ]. Below, we focus on the currently identified uracil-DNA glycosylase inhibitors.…”

Section: Ung Inhibitors and Their Potential Biotechnological Applicationsmentioning

confidence: 99%

Viruses with U-DNA: New Avenues for Biotechnology

Nagy

Skurnik

Vértessy

2021

Viruses

View full text Add to dashboard Cite

Deoxyuridine in DNA has recently been in the focus of research due to its intriguing roles in several physiological and pathophysiological situations. Although not an orthodox DNA base, uracil may appear in DNA via either cytosine deamination or thymine-replacing incorporations. Since these alterations may induce mutation or may perturb DNA–protein interactions, free living organisms from bacteria to human contain several pathways to counteract uracilation. These efficient and highly specific repair routes uracil-directed excision repair initiated by representative of uracil-DNA glycosylase families. Interestingly, some bacteriophages exist with thymine-lacking uracil-DNA genome. A detailed understanding of the strategy by which such phages can replicate in bacteria where an efficient repair pathway functions for uracil-excision from DNA is expected to reveal novel inhibitors that can also be used for biotechnological applications. Here, we also review the several potential biotechnological applications already implemented based on inhibitors of uracil-excision repair, such as Crispr-base-editing and detection of nascent uracil distribution pattern in complex genomes.

show abstract

Section: Ung Inhibitors and Their Potential Biotechnological Applicationsmentioning

confidence: 99%

Viruses with U-DNA: New Avenues for Biotechnology

Nagy

Skurnik

Vértessy

2021

Viruses

View full text Add to dashboard Cite

show abstract

“…For example, phage T7 Ocr can protect phage DNA from bacterial restriction enzymes and the BREX (BacteRiophage EXclusion) defense system [5,6]. Staphylococcus aureus SAUGI strongly inhibits the DNA repair activity of the uracil DNA glycosylase (UDG) of various species [7][8][9]; this DNA mimic protein has also been suggested to participate in the transfer of Staphylococcal DNA element (SCCmec) between methicillin-resistant S. aureus strains [10]. Neisseria meningitidis DMP19 modulates transcription and nucleoid formation through different oligomer states [11,12].…”

Section: Introductionmentioning

confidence: 99%

A Novel Relative Distance Protein Fingerprint Algorithm for Searching DNA Mimic Proteins

Chien

Chou

Hsu

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Backgground: DNA mimic proteins are relatively obscure control factors that share some similarities with DNA. They emulate the negative charge distribution of the phosphate backbone of DNA by using negatively charged amino acids, namely, aspartic acids (ASP or D) and glutamic acids (GLU or E). Known DNA mimic proteins control various cellular mechanisms, such as transcription, DNA repair, and gene regulation, by intervening in the binding of DNA to effector proteins. In addition to being functionally important, DNA mimic proteins have potential for use in biotechnological applications. For example, the DNA mimic protein AcrIIA4 from Listeria monocytogenes prophages can improve the accuracy of gene editing by controlling the activity of CRISPR-Cas9. Therefore, DNA mimic proteins warrant further research. However, most DNA mimic proteins cannot be identified using traditional bioinformatics methods owing to their unique amino acid sequences and structural features. Results: We developed a new protein fingerprint, called relative distance protein fingerprint (RD-PFP), that can be used to analyze the distribution of amino acids on a protein surface. We optimized our RD-PFP by using machine learning and the characteristic feature of DNA mimic proteins (namely, their DNA-like negative charge distribution) to more accurately predict DNA mimicry from protein sequences. Conclusion: Our pioneering study contributes to the development of machine learning--based bioinformatics methods for screening DNA mimic proteins.

show abstract

Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases

Cited by 2 publications

References 39 publications

Viruses with U-DNA: New Avenues for Biotechnology

Viruses with U-DNA: New Avenues for Biotechnology

A Novel Relative Distance Protein Fingerprint Algorithm for Searching DNA Mimic Proteins

Contact Info

Product

Resources

About