F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif
Abstract Background There are six known families of homing endonucleases, LAGLIDADG, GIY-YIG, HNH, His-Cys box, PD-(D/E)-XK, and EDxHD, which are characterized by their conserved residues. Previously, we discovered a novel homing endonuclease F-CphI encoded by ORF177 of cyanophage S-PM2. F-CphI does...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-08-01
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| Series: | Mobile DNA |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13100-018-0132-5 |
| _version_ | 1819011555225763840 |
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| author | Xiaoting Fang YongLiang Jiang Kim Li Qinglu Zeng |
| author_facet | Xiaoting Fang YongLiang Jiang Kim Li Qinglu Zeng |
| author_sort | Xiaoting Fang |
| collection | DOAJ |
| description | Abstract Background There are six known families of homing endonucleases, LAGLIDADG, GIY-YIG, HNH, His-Cys box, PD-(D/E)-XK, and EDxHD, which are characterized by their conserved residues. Previously, we discovered a novel homing endonuclease F-CphI encoded by ORF177 of cyanophage S-PM2. F-CphI does not resemble any characterized homing endonucleases. Instead, the C-terminus of F-CphI aligns well with the N-terminal catalytic domain of a Holliday junction DNA resolvase, phage T4 endonuclease VII (Endo VII). Results A PSI-BLAST search resulted in a total of 313 Endo VII motif–containing sequences in sequenced genomes. Multiple sequence alignment showed that the catalytically important residues of T4 Endo VII were all well conserved in these proteins. Our site-directed mutagenesis studies further confirmed that the catalytically important residues of T4 Endo VII were also essential for F-CphI activity, and thus F-CphI might use a similar protein fold as Endo VII for DNA cleavage. A phylogenetic tree of the Endo VII motif–containing sequences showed that putative resolvases grouped into one clade while putative homing endonucleases and restriction endonucleases grouped into another clade. Conclusions Based on the unique conserved residues, we proposed that F-CphI represents a new homing endonuclease family, which was named the DHHRN family. Our phylogenetic analysis could be used to predict the functions of many previously unknown proteins. |
| first_indexed | 2024-12-21T01:30:01Z |
| format | Article |
| id | doaj.art-03c6b8f31c994ce68556730acf4b8b9f |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-12-21T01:30:01Z |
| publishDate | 2018-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-03c6b8f31c994ce68556730acf4b8b9f2022-12-21T19:20:23ZengBMCMobile DNA1759-87532018-08-019111110.1186/s13100-018-0132-5F-CphI represents a new homing endonuclease family using the Endo VII catalytic motifXiaoting Fang0YongLiang Jiang1Kim Li2Qinglu Zeng3Department of Ocean Science, The Hong Kong University of Science and TechnologySchool of Life Sciences, University of Science and Technology of ChinaDepartment of Ocean Science, The Hong Kong University of Science and TechnologyDepartment of Ocean Science, The Hong Kong University of Science and TechnologyAbstract Background There are six known families of homing endonucleases, LAGLIDADG, GIY-YIG, HNH, His-Cys box, PD-(D/E)-XK, and EDxHD, which are characterized by their conserved residues. Previously, we discovered a novel homing endonuclease F-CphI encoded by ORF177 of cyanophage S-PM2. F-CphI does not resemble any characterized homing endonucleases. Instead, the C-terminus of F-CphI aligns well with the N-terminal catalytic domain of a Holliday junction DNA resolvase, phage T4 endonuclease VII (Endo VII). Results A PSI-BLAST search resulted in a total of 313 Endo VII motif–containing sequences in sequenced genomes. Multiple sequence alignment showed that the catalytically important residues of T4 Endo VII were all well conserved in these proteins. Our site-directed mutagenesis studies further confirmed that the catalytically important residues of T4 Endo VII were also essential for F-CphI activity, and thus F-CphI might use a similar protein fold as Endo VII for DNA cleavage. A phylogenetic tree of the Endo VII motif–containing sequences showed that putative resolvases grouped into one clade while putative homing endonucleases and restriction endonucleases grouped into another clade. Conclusions Based on the unique conserved residues, we proposed that F-CphI represents a new homing endonuclease family, which was named the DHHRN family. Our phylogenetic analysis could be used to predict the functions of many previously unknown proteins.http://link.springer.com/article/10.1186/s13100-018-0132-5Homing endonucleaseGroup I intronF-CphIEndonuclease VIIBacteriophage |
| spellingShingle | Xiaoting Fang YongLiang Jiang Kim Li Qinglu Zeng F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif Mobile DNA Homing endonuclease Group I intron F-CphI Endonuclease VII Bacteriophage |
| title | F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif |
| title_full | F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif |
| title_fullStr | F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif |
| title_full_unstemmed | F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif |
| title_short | F-CphI represents a new homing endonuclease family using the Endo VII catalytic motif |
| title_sort | f cphi represents a new homing endonuclease family using the endo vii catalytic motif |
| topic | Homing endonuclease Group I intron F-CphI Endonuclease VII Bacteriophage |
| url | http://link.springer.com/article/10.1186/s13100-018-0132-5 |
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