Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)

In order to cope with the risk of stress-induced mutagenesis, cells in all kingdoms of life employ Y-family DNA polymerases to resolve resulting DNA lesions and thus maintaining the integrity of the genome. In Escherichia coli, the DNA polymerase IV, or DinB, plays this crucial role in coping with these type of mutations via the so-called translesion DNA synthesis. Despite the availability of several high-resolution crystal structures, important aspects of the functional repertoire of DinB remain elusive. In this study, we use advanced solution NMR spectroscopy methods in combination with biophysical characterization to elucidate the crucial role of the Thumb domain within DinB's functional cycle. We find that the inherent dynamics of this domain guide the recognition of double-stranded (ds) DNA buried within the interior of the DinB domain arrangement and trigger allosteric signals through the DinB protein. Subsequently, we characterized the RNA polymerase interaction with DinB, revealing an extended outside surface of DinB and thus not mutually excluding the DNA interaction. Altogether the obtained results lead to a refined model of the functional repertoire of DinB within the translesion DNA synthesis pathway.

Automated summary

To deal with the risk of stress-induced mutagenesis, cells employ Y-family DNA polymerases to repair DNA lesions and maintain genome integrity. In Escherichia coli, DNA polymerase IV, or DinB, is crucial for coping with these mutations through translesion DNA synthesis. However, important aspects of DinB's functional repertoire still remain elusive. This study used advanced solution NMR spectroscopy methods and biophysical characterization to elucidate the role of the Thumb domain in DinB's functional cycle, providing insights into its interaction with DNA and RNA polymerase.