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A protein architecture guided screen for modification dependent restriction endonucleases
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 s...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765204/ https://www.ncbi.nlm.nih.gov/pubmed/31504772 http://dx.doi.org/10.1093/nar/gkz755 |
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author | Lutz, Thomas Flodman, Kiersten Copelas, Alyssa Czapinska, Honorata Mabuchi, Megumu Fomenkov, Alexey He, Xinyi Bochtler, Matthias Xu, Shuang-yong |
author_facet | Lutz, Thomas Flodman, Kiersten Copelas, Alyssa Czapinska, Honorata Mabuchi, Megumu Fomenkov, Alexey He, Xinyi Bochtler, Matthias Xu, Shuang-yong |
author_sort | Lutz, Thomas |
collection | PubMed |
description | 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 Escherichia 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. |
format | Online Article Text |
id | pubmed-6765204 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-67652042019-10-02 A protein architecture guided screen for modification dependent restriction endonucleases Lutz, Thomas Flodman, Kiersten Copelas, Alyssa Czapinska, Honorata Mabuchi, Megumu Fomenkov, Alexey He, Xinyi Bochtler, Matthias Xu, Shuang-yong Nucleic Acids Res Nucleic Acid Enzymes 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 Escherichia 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. Oxford University Press 2019-10-10 2019-09-03 /pmc/articles/PMC6765204/ /pubmed/31504772 http://dx.doi.org/10.1093/nar/gkz755 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Nucleic Acid Enzymes Lutz, Thomas Flodman, Kiersten Copelas, Alyssa Czapinska, Honorata Mabuchi, Megumu Fomenkov, Alexey He, Xinyi Bochtler, Matthias Xu, Shuang-yong A protein architecture guided screen for modification dependent restriction endonucleases |
title | A protein architecture guided screen for modification dependent restriction endonucleases |
title_full | A protein architecture guided screen for modification dependent restriction endonucleases |
title_fullStr | A protein architecture guided screen for modification dependent restriction endonucleases |
title_full_unstemmed | A protein architecture guided screen for modification dependent restriction endonucleases |
title_short | A protein architecture guided screen for modification dependent restriction endonucleases |
title_sort | protein architecture guided screen for modification dependent restriction endonucleases |
topic | Nucleic Acid Enzymes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765204/ https://www.ncbi.nlm.nih.gov/pubmed/31504772 http://dx.doi.org/10.1093/nar/gkz755 |
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