Genome quality control: RIP (repeat‐induced point mutation) comes to Podospora

Abstract

RIP (repeat‐induced point mutation) is a silencing process discovered in Neurospora crassa and so far clearly established only in this species as a currently occurring process. RIP acts premeiotically on duplicated sequences, resulting in C‐G to T‐A mutations, with a striking preference for CpA/TpG dinucleotides. In Podospora anserina, an RIP‐like event was observed after several rounds of sexual reproduction in a strain with a 40 kb tandem duplication resulting from homologous integration of a cosmid in the mating‐type region. The 9 kb sequenced show 106 C‐G to T‐A transitions, with 80% of the replaced cytosines located in CpA dinucleotides. This led to the alteration of at least six genes, two of which were unidentified. This RIP‐like event extended to single‐copy genes between the two members of the repeat. The overall data show that the silencing process is strikingly similar to a light form of RIP, unaccompanied by C‐methylation. Interestingly, the N. crassa zeta–eta sequence, which acts as a potent de novo C‐methylation RIP signal in this species, is weakly methylated when introduced into P. anserina. These results demonstrate that RIP, at least in light forms, can occur beyond N. crassa.

The genome sequence of the filamentous fungus Neurospora crassa

“…Finally, the genome sequence has revealed the remarkable impact of RIP on the evolution of genes in Neurospora. Recent reports indicating the apparent presence of RIP in other fungi 67,68 broaden the implications of our findings. The apparent lack of functional gene duplication in Neurospora provides a unique opportunity to study other modes of evolution in this experimentally tractable organism.…”

Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation

“…RIP has originally been discovered in N. crassa where it inactivates duplicated sequences during the sexual phase of the life cycle (Selker et al, 1987). It was also shown to exist in a milder form in Podospora anserina (Graia et al, 2001;Hamann et al, 2000) and Magnaporthe grisea (Ikeda et al, 2002). RIP is thought to be responsible for the surprisingly low number of multigene families and duplicated sequences observed in N. crassa (Galagan et al, 2003).…”

Repetitive DNA sequences include retrotransposons in genomes of the Glomeromycota

“…The transitions observed in the GmarRT1 retrotransposon family are reminiscent of repeated-induced point mutations (RIP), a premeiotic inactivation process of repetitive elements occurring in the fungus Neurospora crassa (Selker and Stevens 1985). RIP-like transitions have also been reported in transposable elements of other Ascomycetes such as Aspergillus fumigatus (Neuveglise et al 1996), A. nidulans (Nielsen et al 2001), Fusarium oxysporum (Hua- Van et al 1998), Magnaporthe grisea (Nakayashiki et al 1999), Podospora anserina (Graia et al 2001), Leptosphaeria maculans (Attard et al 2005), Epichloe festucae (Young et al 2005) and Basidiomycetes like Microbotryum violaceum (Hood et al 2005). Inactivation of transposable elements by this process can serve as a defence mechanism in the genome against mobile repetitive elements which would otherwise result in a large increase in genome size (Hsieh and Fire 2000).…”