Repeat-Induced Point Mutation in Fungi: A Fungal-Specific Endogenous Mutagenesis Process

Abstract

Repeat-induced point mutation (RIP) is a form of genome mutation that is targeted towards repeated DNA sequences and which is observed only in certain fungal taxa; the Pezizomycotina (filamentous Ascomycota) and some species of the Basidiomycota. RIP is widely believed to have evolved to protect fungal genomes against transposon replication.RIP was first observed during the sexual reproductive cycle of the ascomycete Neurospora crassa. During the haploid dikaryotic stage that occurs following fertilization and prior to meiosis, the RIP process selectively mutated duplicated sequences in both DNA strands by inducing single-nucleotide point (SNP) mutations that converted C:G base pairs to T:A. This often led to the introduction of nonsense or missense mutations which affected the expression of these sequences. The precise mechanism by which detection and subsequent mutation of duplicated regions occurs is still unknown, but is dependent on a cytosine methyltransferase.RIP has also been observed to influence the evolution of fungal genes. With the exception of ribosomal DNA repeats, RIP acts upon repeated genomic regions including tandem repeats, unlinked repeats, and large segmental duplications including endogenous genes. RIP has the potential to either enhance or impede the generation of genetic diversity. Species exhibiting high levels of RIP are observed to be deficient in gene family diversity, whereas diversity among gene families in species with low levels of RIP is increased. Furthermore, RIP has also been reported to affect non-duplicated genes adjacent to RIP-affected repetitive DNA sequences, which may drive the evolution of these genes and can promote rapid adaptation to selection pressures in some species.