Institute for Cell and Molecular Biosciences (ICaMB), University of Newcastle, Newcastle upon Tyne NE2 4HH, UK.
Published: February 2009
AI Article Synopsis
Article Abstract
Archaeal family-B DNA polymerases interact specifically with uracil and hypoxanthine, stalling replication on encountering these deaminated bases in DNA template strands. The present review describes X-ray structural data which elucidate the mechanism of read-ahead recognition of uracil and suggests how this is coupled to cessation of polymerization. The possible role of read-ahead recognition of uracil/hypoxanthine in DNA repair is discussed, as is the observation that the feature appears to be limited to replicative polymerases of the archaeal domain.
DNA deaminase toxins, like the single-stranded DNA deaminase SsdA, play roles in bacterial competition and genetic diversity while also serving as tools for genome engineering.
The crystal structure of SsdA bound to single-stranded DNA shows a unique binding mode that allows for broad substrate selectivity, characterized by a V-shaped conformation around the target cytosine.
Key findings include the identification of a β-amino acid isoaspartate in SsdA that's crucial for its activity and stability, paving the way for engineered mutants that could be used in human cells for future genome editing applications.
The generation of DNA damage causes mutations and consequently cancer. Reactive oxygen species are important sources of DNA damage and some mutation signatures found in human cancers. 8-Oxo-7,8-dihydroguanine (G, 8-hydroxyguanine) is one of the most abundant oxidized bases and induces a G→T transversion mutation at the modified site.
Deamination of bases is a form of DNA damage that occurs spontaneously via the hydrolysis and nitrosation of living cells, generating hypoxanthine from adenine. E. coli endonuclease V (eEndoV) cleaves hypoxanthine-containing double-stranded DNA, whereas human endonuclease V (hEndoV) cleaves hypoxanthine-containing RNA; however, hEndoV in vivo function remains unclear.
One of the most recent advances in the genome editing field has been the addition of "TALE Base Editors", an innovative platform for cell therapy that relies on the deamination of cytidines within double strand DNA, leading to the formation of an uracil (U) intermediate. These molecular tools are fusions of transcription activator-like effector domains (TALE) for specific DNA sequence binding, split-DddA deaminase halves that will, upon catalytic domain reconstitution, initiate the conversion of a cytosine (C) to a thymine (T), and an uracil glycosylase inhibitor (UGI). We developed a high throughput screening strategy capable to probe key editing parameters in a precisely defined genomic context in cellulo, excluding or minimizing biases arising from different microenvironmental and/or epigenetic contexts.
The AID/APOBECs are a group of zinc-dependent cytidine deaminases that catalyse the deamination of bases in nucleic acids, resulting in a cytidine to uridine transition. Secreted novel AID/APOBEC-like deaminases (SNADs), characterized by the presence of a signal peptide are unique among all of intracellular classical AID/APOBECs, which are the central part of antibody diversity and antiviral defense. To date, there is no available knowledge on SNADs including protein characterization, biochemical characteristics and catalytic activity.
