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Evolution of LAGLIDADG Homing Endonucleases Residing in Fungal Mitochondrial Cob

Author: ChenZhiGang
Tutor: FanSanHong
School: Northwest University of Science and Technology
Course: Bioinformatics
Keywords: fungal mitochondria cob homing endonuclease LAGLIDADG domain evolution
CLC: Q75
Type: Master's thesis
Year: 2013
Downloads: 15
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Abstract


Mitochondrial genome size varies dramatically in fungi. The size of mitochondrialgenome is156kb in Phlebia radiata while only19kb in Hanseniaspora uvarum. Thedifference mainly arises from distinct numbers of self-splicing introns in conservedmitochondrial genes. Cytochrome b (cob) is one of such genes and encodes a subunit ofcytochrome reductive complex in respiratory. LAGLIDADG homing endonucleases areDNA-incision enzymes parasitizing in self-splicing introns and promote their host intronsspread through homing process. LAGLIDADG homing endonucleases usually recognize12-40bp target sequences with extremely high specificity; in consequence, they can serve astool enzymes in gene therapy and targeted gene modification.In this study, based on114published mitochondria genomes of fungi and LAGLIDADGhoming endonuclease sequences in Pfam database, we analyzed type Ⅰ double-domainLAGLIDADG homing endonucleases and type Ⅱ LAGLIDADG homing endonucleases incob introns systematically, with the purpose of uncovering the evolution pattern and findingsome homing endonucleases having potential function as native scaffolds for designing anddeveloping of gene-targeting enzymes. The result of this study was as follows:There were224type Ⅰd ouble-domain LAGLIDADG homing endonucleases and72typeII LAGLIDADG homing endonucleases in fungal mitochondria genomes, primarilydistributing in three mitochondrial genes(cob, cox1and nad5). Introns of cob respectivelyencoded24type I double-domain and27type II LAGLIDADG homing endonucleases. Genestructure analysis indicated that12type I double-domain LAGLDIADG homingendonuclease distributed in adjacent intron insertion sites: S506，S507，S508，S510，S511andS514(S506-S514), other12scattered in7remote sites, while18type II LAGLIDADGhoming endonucleases inserted in S433and other9scattered in8intron insertion sites.Cluster analysis showed that the two kinds of LAGLIDADG homing endonuclease couldbe divided into34and10groups, respectively.11type I double-domain LAGLIDADGhoming endonucleases in S506-S514and18type II LAGLIDADG homing endonucleases inS433were located in identical groups, which demonstrated that both of them had close genetic relationship, respectively. Both Type I and type II LAGLIDADG homingendonucleases had horizontal transfer among speices in different kingdoms and differentgenes in fungal mitochondria. Phylogenetic analysis showed ancestral sequence of15type Idouble-domain LAGLIDADG homing endonucleases in S506-S514and S722undergoneLAGLIDADG domain replication in evolution history, while other homing endonucleaseswere inferred that single domain might lose and reinsert accompanying with replication.18type II LAGLIDADG homing endonucleases encoded by S433site coupled with host intronsshould vertical inherited from common ancestor accompanied by horizontal gene transferfrom time to time; other homing endonucleases in cob introns were inferred as a result oflateral transfer only. Three groups which had homing endonucleases in cob manifested thattheir target sequences presented apparent difference, analyzing of conserved amino acids inLAGLIDADG motif indicated that most of them had potential cleaving activity and could beused as scaffold applying in gene modifying.We presented a whole landscape and evolutionary pattern of introns and intronic type Idouble-domain and type II LAGLIDADG homing endonucleases residing in fungalmitochondrial cob, we also provided new scaffolds for modifying and redesigning of homingendonucleases.

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