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A protein architecture guided screen for modification dependent restriction endonucleases

Lutz, Thomas and Flodman, Kiersten and Copelas, Alyssa and Czapinska, Honorata and Mabuchi, Megumu and Fomenkov, Alexey and He, Xinyi and Bochtler, Matthias and Xu, Shuang-yong (2019) A protein architecture guided screen for modification dependent restriction endonucleases. Nucleic Acids Research, 47 (18). pp. 9761-9776. ISSN 0305-1048

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Abstract

Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI), and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5 methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featuring a PUA superfamily domain, but of a different clade, exhibited 6-methyladenine stimulated nicking activity. With few exceptions, ORFs for PUA-superfamily domain containing endonucleases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activity of the endonucleases. DUF3427 domain containing fusion proteins had very little or no endonuclease activity, despite the presence of a putative PD-(D/E)XK catalytic domain. However, their expression potently restricted phage T4gt in E. coli cells. In contrast to the ORFs for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found in defense islands, often also featuring DNA methyltransferases.

Item Type:Article
Subjects:Q Science > Q Science (General)
Divisions:Department of Bioinformatics
ID Code:1779
Deposited By: Prof. Matthias Bochtler
Deposited On:06 Dec 2019 08:25
Last Modified:06 Dec 2019 08:25

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