Repeat induced point mutation in two asexual fungi, Aspergillus niger and Penicillium chrysogenum

Abstract

Repeat induced point mutation (RIP) is a gene silencing mechanism present in fungal genomes. During RIP, duplicated sequences are efficiently and irreversibly mutated by transitions from C:G to T:A. For the first time, we have identified traces of RIP in transposable elements of Aspergillus niger and Penicillium chrysogenum, two biotechnologically relevant fungi. We found that RIP in P. chrysogenum has affected a large set of sequences, which also contain other mutations. On the other hand, RIP in A. niger is limited to only few sequences, but literally all mutations are RIP-like. Surprisingly, RIP occurred only in transposon sequences that have disrupted open reading frames in A. niger, a phenomenon not yet reported for other fungi. In both fungal species, we identified two sequences with strong sequence similarity to Neurospora crassa RID. RID is a putative DNA methyltransferase and the only known enzyme involved in the RIP process. Our findings suggest that both A. niger and P. chrysogenum either had a sexual past or have a sexual potential. These findings have important implications for future strain development of these fungi.

Presence and Functionality of Mating Type Genes in the Supposedly Asexual Filamentous Fungus Aspergillus oryzae

“…We have also observed the expression of pheromone precursor and receptor genes, and elements of a pheromone response mitogen-activated protein (MAP) kinase signal transduction pathway, in two MAT1-1 (AO46 and AO10) and two MAT1-2 (AO6 and AO8) A. oryzae isolates of complementary mating types (M. Paoletti, E. U. Schwier, and P. S. Dyer, unpublished data). In addition, there is evidence of previous sexual reproduction by A. oryzae based on analysis of repeat-induced point mutations (RIP) in the genome (44), as also observed for the asexual species Aspergillus niger and Penicillium chrysogenum (5). Furthermore, sexual cycles have recently been detected in both A. flavus and A. parasiticus (25,27), which are phylogenetically very closely related to A. oryzae (43,52), and it has been suggested that A. flavus is an ancestor of A. oryzae (20).…”

Sexual reproduction and mating-type–mediated strain development in the penicillin-producing fungus Penicillium chrysogenum

“…Significantly, a MAT1-1 locus, with a MAT1-1-1 gene encoding a putative alpha-box transcription factor, is present in NRRL1951 and all its derivatives, whereas the original Fleming strain contains the opposite MAT1-2 locus (10). In addition, recombination has been reported within natural populations of P. chrysogenum together with a near 1:1 distribution of MAT1-1 and MAT1-2 isolates (6), and there is evidence of repeat induced point mutation in the genome, a process associated with meiosis (12).…”

Fungal Transposable Elements

“…In the A. niger strain CBS513.88 e.g. fi ve copies of the ANiTa family were found with one differing from the others by one transversion and multiple transitions (Braumann et al 2008 ).…”