Structural and Functional Characteristics of Homing Endonucleases

Abstract

Mobile genetic elements constitute a remarkably diverse group of nonessential selfish genes that provide no apparent function to the host. These selfish genes have been implicated in host extinction, speciation and architecture of genetic systems. Homing endonucleases, encoded by the open reading frames embedded in introns or inteins of mobile genetic elements, possess double-stranded DNA-specific endonuclease activity. They inflict sequence-specific double-strand breaks at or near the homing site in intron- or intein-less allele. Subsequently, through nonreciprocal exchange the insertion sequence (intron or intein) is transferred from an intein- or intron-containing allele to an intein- or intron-less allele. The components of host double-strand break repair pathway are thought to finish the "homing" process. Several lines of evidence suggest that homing endonucleases are capable of promoting transposition into ectopic sites within or across genomes for their survival as well as dispersal in natural populations. The occurrence of inteins at high frequencies serves as instructive models for understanding the mechanistic aspects of the process of homing and its evolution. This review focuses on genetic, biochemical, structural, and phylogenetic aspects of homing endonucleases, and their comparison with restriction endonucleases.

Mutational analysis of active‐site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp122 and Asp193 are crucial to the double‐stranded DNA cleavage activity whereas Asp218 is not

“…[1][2][3][4][5][6] These enzymes confer mobility to genetic determinants by a gene conversion event termed ''homing.'' [1][2][3][4][5][6] During the homing process, the endonuclease inflicts a double-strand break at or near the homing site of the intein-/intron-less allele, which is subsequently repaired by the host DNA repair machinery resulting in the inheritance of intein/intron. [1][2][3][4][5][6] Consequently, efforts are being made to explore the possibility of using HEases as tools for genome mapping, cloning of megabase DNA fragments, and gene targeting.…”

“…[1][2][3][4][5][6] During the homing process, the endonuclease inflicts a double-strand break at or near the homing site of the intein-/intron-less allele, which is subsequently repaired by the host DNA repair machinery resulting in the inheritance of intein/intron. [1][2][3][4][5][6] Consequently, efforts are being made to explore the possibility of using HEases as tools for genome mapping, cloning of megabase DNA fragments, and gene targeting. 1,7,8 One hallmark of HEases is their ability to recognize and cleave long DNA target sites (14-40 bp) spanning their insertion site in the intron-/ intein-less allele.…”

“…1,7,8 One hallmark of HEases is their ability to recognize and cleave long DNA target sites (14-40 bp) spanning their insertion site in the intron-/ intein-less allele. [1][2][3][4][5][6] The family of HEases is divided into four subfamilies based on the primary structure of their active site motifs: LAGLIDADG, GIY-YIG, H-N-H, and His-Cys box families. [1][2][3][4][5][6] Recently, the list of HEases is expanded with the addition of PD-(D/E)-XK nuclease family.…”

“…[1][2][3][4][5][6] The family of HEases is divided into four subfamilies based on the primary structure of their active site motifs: LAGLIDADG, GIY-YIG, H-N-H, and His-Cys box families. [1][2][3][4][5][6] Recently, the list of HEases is expanded with the addition of PD-(D/E)-XK nuclease family. 9 Among these, LAGLI-DADG family is the largest, most prevalent, and well-studied class.…”

“…9 Among these, LAGLI-DADG family is the largest, most prevalent, and well-studied class. [1][2][3][4][5][6] HEases that contain a single copy of LAGLIDADG motif per polypeptide chain, such as I-CreI, I-MsoI, and I-CeuI, function as homodimers and recognize and cleave palindromic and pseudo-palindromic DNA sequences. [3][4][5] On the other hand, HEases that harbor two copies of LAGLIDADG motifs, including I-AniI, PI-SceI, and I-SceI, act as monomers and recognize and cleave their DNA target sites with considerable asymmetry.…”