Abstract
Homing endonucleases (HE) are enzymes capable of cutting DNA at highly specific target sequences, the repair of the generated double‐strand break resulting in the insertion of the HE‐encoding gene (“homing” mechanism). HEs are present in all three domains of life and viruses; in eukaryotes, they are mostly found in the genomes of mitochondria and chloroplasts, as well as nuclear ribosomal RNAs. We here report the case of a HE that accidentally integrated into a telomeric region of the nuclear genome of the fungal maize pathogen Ustilago maydis. We show that the gene has a mitochondrial origin, but its original copy is absent from the U. maydis mitochondrial genome, suggesting a subsequent loss or a horizontal transfer from a different species. The telomeric HE underwent mutations in its active site and lost its original start codon. A potential other start codon was retained downstream, but we did not detect any significant transcription of the newly created open reading frame, suggesting that the inserted gene is not functional. Besides, the insertion site is located in a putative RecQ helicase gene, truncating the C‐terminal domain of the protein. The truncated helicase is expressed during infection of the host, together with other homologous telomeric helicases. This unusual mutational event altered two genes: The integrated HE gene subsequently lost its homing activity, while its insertion created a truncated version of an existing gene, possibly altering its function. As the insertion is absent in other field isolates, suggesting that it is recent, the U. maydis 521 reference strain offers a snapshot of this singular mutational event.
Highlights
The elucidation of the mechanisms at the origin of genetic variation is a longstanding goal of molecular evolutionary biology
We report the analysis of the nuclear gene UMAG_11064 from the smut fungus U. maydis, which was identified as an outlier in a whole-genome analysis of codon usage
We first provide evidence that the gene is a former homing endonuclease genes (HEG) and reconstruct the molecular events that led to its insertion in the nuclear genome using comparative sequence analysis
Summary
The elucidation of the mechanisms at the origin of genetic variation is a longstanding goal of molecular evolutionary biology. Mutation accumulation experiments - together with comparative analysis of sequence data - are instrumental in studying the processes shaping genetic diversity at the molecular level (Kondrashov and Kondrashov 2010; Eyre-Walker and Keightley 2007). Mutations can be caused or favored by extrinsic factors, such as mutagenic environmental conditions or parasitic genome entities like viruses or selfish mobile elements Such particular sequences, able to replicate and invade the host genome, may have various effects including inserting long stretches of DNA that do not encode any organismic function, and disrupting, copying and moving parts of the genome sequence. Control mechanisms (such as repeat-induced point mutations in fungi (Gladyshev 2017)) may incidentally affect genetic diversity (Grandaubert et al 2014)
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