Biology subjects

Salzberg, L. I.

Publications and source records attributed to Salzberg, L. I..

3 recordsLinked to original sources

bioRxiv2025

Zymocin-like killer plasmids were present in the common ancestor of terrestrial fungi

Some budding yeasts secrete killer toxins made by linear dsDNA plasmids located in the cytosol. The best-known example is the Kluyveromyces lactis toxin zymocin, which is encoded by a 9-kb killer plasmid assisted by a 13-kb helper plasmid. These plasmids are distantly related to eukaryotic dsDNA viruses and have been called Virus-Like Elements (VLEs) but they do not produce virus particles. Their evolutionary origin is unclear because VLEs have been found only in budding yeasts (subphylum Saccharomycotina of phylum Ascomycota) and not in any other fungi. Here, we show that similar VLEs are present in two deeply divergent phyla of terrestrial fungi, Zoopagomycota and Mucoromycota. In Zoopagomycota, some isolates of Coemansia harbor more than 20 different linear dsDNA plasmids simultaneously, many of which encode their own DNA polymerases (DNAPs). We did not identify any functional killer toxins encoded by the new VLEs, but phylogenetic analysis of the chitinase genes present on some of them suggests that they are orthologs of the chitinase subunits of killer toxins encoded by Saccharomycotina VLEs. Phylogenetic analysis of DNAPs shows that the diversity of VLEs in Zoopagomycota greatly exceeds that in Saccharomycotina, and that Saccharomycotina killer and helper plasmids are related to two lineages of VLEs present in Zoopagomycota. Our results indicate that VLEs were present in the common ancestor of all terrestrial fungi about 650 Mya, and that they were already subdivided into killer and helper types by this time.

evolutionary biology↗

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↗