A killer is revealed: kambucha yeast poison their competitors

Science Spotlight

A killer is revealed: kambucha yeast poison their competitors

From the Malik, Smith, and Zanders Laboratories (Basic Sciences Division, Fred Hutch and the Stowers Institute)

Sept. 18, 2017

Infertility can be caused by defective gametes, called eggs and sperm in humans. Gametes are the products of a unique cell division program named meiosis that generates cells with only one copy of each gene. Much of our understanding of this process comes from studying model single-celled eukaryotes such as the yeast Schizosaccharomyces pombe. Interestingly, hybrids of S. pombe and its close relative S. kambucha (99.5% identical at the nucleotide level1) can be formed but are sterile, producing only infertile gametes. Previous research in the Malik and Smith Laboratories (Basic Sciences Division), driven by Dr. SaraH Zanders, now a faculty member at Stowers Institute for Medical Research (Kansas City, MO), determined that selfish genes contribute to this hybrid sterility2. Selfish genes are so-named because they are inherited more often than would be expected by chance; thus, they appear to 'bias' reproduction in their favor so that they can spread and persist while the unselfish version of the gene is outcompeted. While a large body of evidence supports the existence of such genes, only a handful have been mapped, sequenced, and characterized. In their latest study published in eLife, Zanders and her colleagues identified and characterized one such selfish gene, called wtf4, named for its association with Tf transposons, another type of selfish gene. It biases its transmission to gametes in S.pombe/S. kambucha hybrids through an intriguing new mechanism: the gene encodes alternative transcripts which encode a "poison" that is released from the cell and an "antidote" that protects the cell expressing the gene.

The scientists had previously found that S.pombe/S.kambucha hybrids produce the normal number of gametes but gametes that inherit S. pombe genes die preferentially. Selfish genes that act to ensure they are inherited by "driving" the process of meiosis in their favor are called meiotic drive genes. Based on this previous work, the scientists knew that a meiotic drive gene was present on chromosome 3 of S. kambucha but not on that of S. pombe. To find the location and identity of the meiotic drive gene, the scientists generated a synthetic haploid strain that had S. kambucha chromosomes 1 and 2 but had a mostly S. pombe chromosome 3. They then mated this strain with a pure S. kambucha strain and allowed these cells to carry out meiosis to form gametes. During meiosis, the process of recombination swaps the genes between the chromosomes from each parent to generate unique mosaic chromosomes where parts of each chromosome come from either parent. The S. kambucha/S. pombe hybrids made following this mating therefore each inherited chromosomes 1 and 2 with purely S. kambucha genes but each chromosome 3 was a mixture of S. pombe/S. kambucha genes. The scientists then tracked whether this mosaic chromosome could "drive" its own inheritance by analyzing how often it was inherited by gametes produced from mating a yeast with a mosaic chromosome 3 to a pure S. kambucha strain. The scientists could determine which parts of each mosaic chromosome 3 contained S. pombe genes versus S. kambucha genes by tracking marker genes that were unique to each species. Through this genetic mapping strategy, the authors could identify a mosaic chromosome that had the smallest region of chromosome 3 that could still "drive" itself into gametes and therefore must contain the selfish gene.

Hybrid yeast ascus containing 4 gametes the selfish gene is expressed outside all gametes but only those gametes that inherit the selfish gene express the antidote

S. pombe/S. kambucha ascus containing 4 gametes. Wtf4-GFP is expressed throughout the ascus (diffuse green between the four cells) as well as within 2 out of 4 of the spores (on the right). The two gametes on the left are smaller because they are dying, having inherited S. pombe genes rather than a functional wtf4 from S. kambucha.

Image provided by Dr. Zanders (Stowers Institute)

Click for high-res version

Through further sequence analysis and verification, the scientists identified a gene on S. kambucha chromosome 3 but not present in S. pombe called wtf4. In looking at expression of this gene during meiosis, they found that wtf4 encoded two overlapping transcripts, one longer than the other due to the presence of an alternative start codon. Based on their observations, the scientists hypothesized that one of these transcripts coded for a gene that would act to "poison" all surrounding gametes nonspecifically while the other would work as an "antidote" to the gametes that possessed wtf4. To test this, they labeled the gene on the non-variable end (its C-terminus) with a fluorescent protein to track both the longer and shorter protein products of wtf4. Consistent with their poison-antidote hypothesis, they found fluorescence throughout the ascus, the yeast structure which holds all of the gametes, as well as within only 2 of the 4 gametes produced by a S. pombe/S. kambucha hybrid. Further confirmation of the poison-antidote model came from mutating the alternative start codons of wtf4. They created S. pombe/S. kambucha hybrids where the S. kambucha strain could only make the shorter, poison protein and found that all the gametes died. Conversely, when the S. kambucha strain could only produce the longer, antidote version, there was no evidence for meiotic drive or gamete death.

The scientists analyzed other wtf genes and found another, wtf28, that may behave as a selfish meiotic drive gene.  Other wtf genes that did not "drive" appeared to have mutations that would prevent their expression. Said principal investigator Dr. SaraH Zanders, "In this paper, we were excited to find a whole gene family of gamete-killing meiotic drivers. This wtf family may have been so successful because they use a previously undescribed tactic to kill the competition: the two components required for drive are encoded on alternate transcripts of the same gene. We feel this work is a major advance in our field and will hopefully guide studies of selfish genes in other more complex systems, potentially humans."

 

Nuckolls NL, Bravo Núñez MA, Eickbush MT, Young JM, Lange JJ, Yu JS, Smith GR, Jaspersen SL, Malik HS, Zanders SE. "wtf genes are prolific dual poision-antidote meiotic drivers" eLife.  2017;6:e26033 DOI: 10.7554/eLife.26033

 

Additional citations:

1. Rhind N et al. 2011. "Comparative functional genomics of the fission yeasts." Science. 332:930-936.

2. Zanders SE et al. 2014. "Genome rearrangements and pervasive meiotic drive cause hybrid sterility in fission yeast." eLife. 3:e02630. doi: 10.7554/eLife.02630.

 

This research was supported by funding from the National Institutes of Health, Stowers Institute for Medical Research, G. Harold and Leila Y. Mathers Foundation and Howard Hughes Medical Institute.