New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii

Połomska, Xymena; Neuvéglise, Cécile; Zyzak, Joanna; Żarowska, Barbara; Casarégola, Serge; Lazar, Zbigniew

doi:10.3390/toxins13090615

Cited by 4 publications

(3 citation statements)

References 87 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, the heterogeneity that we found within the single species S. crataegensis (we only found a complete set of full-length plasmids in one of the nine strains we sequenced), and similar heterogeneity in other species (Fukuhara, 1995;Polomska et al, 2021), emphasizes the need to sequence broad panels of environmental isolates to fully uncover the plasmid repertoire of any given species.…”

Section: Discussionmentioning

confidence: 74%

See 1 more Smart Citation

Cytosolic linear DNA plasmids inSaccharomycopsisspecies

Cinnéide

Heneghan

Rajkumar

et al. 2023

Preprint

View full text Add to dashboard Cite

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 alpha/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.

show abstract

Section: Discussionmentioning

confidence: 74%

“…The largest plasmid pScrl-1 is inferred to be a helper plasmid with housekeeping functions similar to K. lactis pGKL2. It contains homologs of all 11 pGKL2 genes (Tommasino et al, 1988;Polomska et al, 2021), in almost the same order (Fig. 1A,B).…”

Section: Genome Sequencing and Data Analysismentioning

confidence: 78%

Cytosolic linear DNA plasmids inSaccharomycopsisspecies

Cinnéide

Heneghan

Rajkumar

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…There was a reverse correlation between sensitivity to both D. hansenii killer toxins and salt resistance (YPD with 4% NaCl). As killer toxin activity is usually measured in the presence of NaCl in the medium [ 55 ], the sensitivity of some strains to NaCl may thus have enhanced their sensitivity to the killer toxins.…”

Section: Resultsmentioning

confidence: 99%

Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica

Bigey

Pasteur

Połomska

et al. 2023

JoF

Self Cite

View full text Add to dashboard Cite

Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.

show abstract

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

Heneghan,

Salzberg,

Cinnéide

et al. 2024

Preprint

View full text Add to dashboard Cite

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.

show abstract

New Cytoplasmic Virus-Like Elements (VLEs) in the Yeast Debaryomyces hansenii

Cited by 4 publications

References 87 publications

Cytosolic linear DNA plasmids inSaccharomycopsisspecies

Cytosolic linear DNA plasmids inSaccharomycopsisspecies

Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica

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

Contact Info

Product

Resources

About