Four additional natural 7-deazaguanine derivatives in phages and how to make them

Cui, L.; Balamkundu, S.; Liu, C. F.; Ye, H.; Hourihan, J.; Rausch, A.; Hauss, C.; Nilsson, E.; Hötzinger, M.; Holmfeldt, K.; Zhang, W.; Martinez-Alvarez, L.; Peng, X.; Tremblay, D.; Moinau, S.; Solonenko, N.; Sullivan, M. B.; Lee, Y.-J.; Mulholland, A.; Weigele, P.; de Crecy-Lagard, V.; Dedon, P. C.; Hutinet, G.

doi:10.1101/2023.04.13.536721

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bioRxiv · 10.1101/2023.04.13.536721

Four additional natural 7-deazaguanine derivatives in phages and how to make them

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Abstract

Bacteriophages and bacteria are engaged in a constant arms race, continually evolving new molecular tools to survive one another. To protect their genomic DNA from restriction enzymes, the most common bacterial defence systems, double-stranded DNA phages have evolved complex modifications that affect all four bases. This study focuses on modifications at position 7 of guanines. Eight derivatives of 7-deazaguanines were identified, including four previously unknown ones: 2-deoxy-7-(methylamino)methyl-7-deazaguanine (mdPreQ1), 2-deoxy-7-(formylamino)methyl-7-deazaguanine (fdPreQ1), 2-deoxy-7-deazaguanine (dDG), and 2-deoxy-7-carboxy-7-deazaguanine (dCDG). These modifications are inserted in DNA by a guanine transglycosylase named DpdA. Three subfamilies of DpdA had been previously characterized: bDpdA, DpdA1, and DpdA2. Two additional subfamilies were identified in this work: DpdA3, which allows for complete replacement of the guanines, and DpdA4, which is specific to archaeal viruses. Transglycosylases have now been identified in all phages and viruses carrying 7-deazaguanine modifications, indicating that the insertion of these modifications is a post-replication event. Three enzymes were predicted to be involved in the biosynthesis of these newly identified DNA modifications: 7-carboxy-7-deazaguanine decarboxylase (DpdL), dPreQ1 formyltransferase (DpdN), and dPreQ1 methyltransferase (DpdM), which was experimentally validated and harbors a unique fold not previously observed for nucleic acid methylases.

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Cui, L., Balamkundu, S., Liu, C. F., Ye, H., Hourihan, J., Rausch, A., Hauss, C., Nilsson, E., Hötzinger, M., Holmfeldt, K., Zhang, W., Martinez-Alvarez, L., Peng, X., Tremblay, D., Moinau, S., Solonenko, N., Sullivan, M. B., Lee, Y.-J., Mulholland, A., Weigele, P., de Crecy-Lagard, V., Dedon, P. C., Hutinet, G.. 2023-04-16. Four additional natural 7-deazaguanine derivatives in phages and how to make them. https://doi.org/10.1101/2023.04.13.536721

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