DAB1: a degenerate retrotransposon-like element from Neurospora crassa

Abstract

A repeated DNA sequence in the genome of Neurospora crassa has been identified as a family of degenerate retroelements. Retroelements encode protein sequences with clear homology to the reverse transcriptase, RNase H and endonuclease products of the pol genes common to retroviruses and retrotransposons. These sequence comparisons place the N. crassa element within the gypsy group of retrotransposons, akin to other elements found in filamentous fungi. However, the Neurospora element is defective, as no flanking long terminal repeats (LTRs) could be distinguished and the pol gene homologues contain numerous stop codons as a result of multiple base substitutions. The base composition of the element displays significant under-representation of the dinucleotide CpA, the preferred target site of repeat-induced point mutation (RIP). The genomic sequences exhibit G:C to A:T transitions between copies which are diagnostic of RIP. The degenerate retroelement has accordingly been designated by the acronym dab-1 (dead and buried).

Degenerate MAGGY elements in a subgroup of Pyricularia grisea: a possible example of successful capture of a genetic invader by a fungal genome

“…Two mechanisms are suggested to be involved in the inactivation process, cytosine methylation and C:G to T:A transitions, both of which are typical features of RIP. Several degenerate fungal transposons have been found, which appear to have been subjected to RIP or RIP-like processes (Schechtman 1990;Julien et al 1992;Kinsey et al 1994;Neuveglise et al 1996;Bibbins et al 1998;HuaVan et al 1998). MRPAN is, however, distinct from the previously reported cases in two respects.…”

“…Thus, it is unclear whether Pyricularia has a functional sexual cycle under natural conditions. There are several reports that RIP-like processes occur in fungal species in which sexual reproduction has not been found (Julien et al 1992;Neuveglise et al 1996;Bibbins et al 1998). It is attractive to assume that C:G to T:A transitions found in these fungal species are relics of RIP that occurred at a time when they had a functional sexual cycle.…”

A family of DNA repeats in Aspergillus nidulans has assimilated degenerated retrotransposons

“…Thus, there seems to be a bias towards mutating cytosines¯anked by 3¢ adenines or 3¢ guanines. Since all but one transition occurred within the Danes, the observed/expected dinucleotide ratio (previously described by Neuveglise et al 1996;Bibbins et al 1998) was calculated for Dane2 and compared with the same ratio for MAGGY. All ratios were similar, with the exception of the value for the CpG dinucleotide, which was 0.57 for Dane2 compared to 1.14 for MAGGY.…”

Neurospora at the Millennium

“…Only one active transposon is known in Neurospora, but inactive DNA sequences have been found that represent different transposon families, and these bear unmistakable hallmarks of RIP (Kinsey et al, 1994;Cambareri et al, 1998;Margolin et al, 1998;Bibbins et al, 1998). Except for one DNA-intermediate element (Yeadon and Catcheside, 1995b), the relic copies of transposable elements discovered so far appear to be retroransposons.…”