Biology subjects

Heneghan, P. G.

Publications and source records attributed to Heneghan, P. G..

3 recordsLinked to original sources

bioRxiv2024

Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi

Zymocin-like killer toxins are anticodon nucleases secreted by some budding yeast species, which kill competitor yeasts by cleaving tRNA molecules. They are encoded by virus-like elements (VLEs), cytosolic linear DNA molecules that are also called killer plasmids. To date, toxins of this type have been found only in budding yeast species (Saccharomycotina). Here, we show that the nuclear genomes of many filamentous fungi (Pezizomycotina) contain small clusters of genes coding for a zymocin-like ribonuclease ({gamma}-toxin), a chitinase (toxin /{beta}-subunit), and in some cases an immunity protein. The {gamma}-toxins from Fusarium oxysporum and Colletotrichum siamense abolished growth when expressed intracellularly in S. cerevisiae. Phylogenetic analysis of glycoside hydrolase 18 (GH18) domains shows that the chitinase genes in the gene clusters are members of the previously described C-II subgroup of Pezizomycotina chitinases. We propose that the Pezizomycotina gene clusters originated by integration of a yeast-like VLE into the nuclear genome, but this event must have been ancient because (1) phylogenetically, the Pezizomycotina C-II chitinases and the Saccharomycotina VLE-encoded toxin /{beta} subunit chitinases are sister clades with neither of them nested inside the other, and (2) many of the Pezizomycotina toxin cluster genes contain introns, whereas VLEs do not. One of the toxin gene clusters in Fusarium graminearum is a locus that has previously been shown to be under diversifying selection in North American populations of this plant pathogen. We also show that two genera of agaric mushrooms (Basidiomycota) have acquired toxin gene clusters by horizontal transfers from different Pezizomycotina donors.

evolutionary biology↗

bioRxiv2024

Ancient origin and high diversity of zymocin-like killer toxins in the budding yeast subphylum

Zymocin is a well-characterized killer toxin secreted by some strains of the yeast Kluyveromyces lactis. It acts by cleaving a specific tRNA in sensitive recipient cells. Zymocin is encoded by a killer plasmid or virus-like element (VLE), which is a linear DNA molecule located in the cytosol. We hypothesized that a tRNA-cleaving toxin similar to zymocin may have caused the three parallel changes to the nuclear genetic code that occurred during yeast evolution, in which the codon CUG became translated as Ser or Ala instead of Leu. However, zymocin-like toxins are rare - both among species, and among strains within a species - and only four toxins of this type have previously been discovered. Here, we identified 45 new zymocin-like toxin genes in Saccharomycotina, the budding yeast subphylum, using a novel bioinformatics strategy, and verified that many of them are toxic to S. cerevisiae when expressed. Some of the new toxin genes are located on cytosolic VLEs, whereas others are on VLE-derived DNA integrated into the nuclear genome. The toxins are extraordinarily diverse in sequence and show evidence of positive selection. Toxin genes were found in five taxonomic orders of budding yeasts, including two of the three orders that reassigned CUG codons, indicating that VLEs have been parasites of yeast species for at least 300 million years and that their existence pre-dates the genetic code changes.

evolutionary biology↗

bioRxiv2023

Cytosolic linear DNA plasmids in Saccharomycopsis species

Some budding yeast species contain cytosolic linear DNA plasmids (also called virus-like elements, VLEs) that code for killer toxins that can kill other yeasts. The toxins are anticodon nucleases that cleave a specific tRNA in the cells being attacked, stopping translation. The best known plasmids of this type are the pGKL1/pGKL2 system of Kluyveromyces lactis. pGKL1 is a killer plasmid encoding the toxin zymocin ({gamma}-toxin) which cleaves tRNA-Glu, and pGKL2 is a helper plasmid required for replication and transcription of pGKL1. Here, we investigated similar plasmids in the genus Saccharomycopsis that were originally described in the 1980s. Saccharomycopsis has undergone an evolutionary change of its genetic code, from CUG-Leu to CUG-Ser translation, which we hypothesized could have been driven by a tRNA-cleaving toxin encoded by a cytosolic plasmid. We sequenced a three-plasmid system in S. crataegensis, consisting of apparent killer, immunity, and helper plasmids. The killer plasmid contains genes coding for putative /{beta} (chitin-binding) and {gamma} (ribonuclease) toxin subunits, but the {gamma}-toxin gene is damaged in all the isolates we examined. We inferred the sequence of the intact S. crataegensis {gamma}-toxin and expressed it in Saccharomyces cerevisiae and Kluyveromyces marxianus, but it did not cause a growth defect. We also identified free plasmids, or plasmids integrated into the nuclear genome, in nine other Saccharomycopsis species, including a case of recent interspecies transfer of a plasmid. Our results show that many yeasts in the CUG-Ser2 clade contain, or have in the past contained, plasmids related to those that carry anticodon nucleases.

evolutionary biology↗