SCAMPRing to get ahead: the enduring battle for supremacy between parasite and host

From the Malik Lab, Basic Sciences Division

For the shield may be as important for victory, as the sword or spear. -Charles Darwin, On the Origin of Species.

In the cutthroat world of natural selection, the struggle for survival has spurred dramatic evolutionary innovations that allow species to survive in nearly unsurvivable environments – those with extreme temperatures, salinities, pressures, or pH – in the quest to find a specialized ecological niche in which to evade predation and outcompete rivals for scarce resources. While many hostile environments have been conquered, the organism with perhaps the most fraught relationship with its niche is the parasite, which has evolved to reside within a living organism, to the dismay and detriment of its unabiding host. What’s so peculiar about this relationship is that the niche fights back. The adaptation of a species to the parasitic way of life sets in motion an intriguing phenomenon: the host species, an evolving entity in its own right that has now been put at a distinct fitness disadvantage, is pressured to adapt itself into a more hostile living environment in an attempt to drive out its unwanted tenant; the stubborn tenant, in turn, rather than take the cue and leave peacefully, is pressured to adapt itself to survive in this new host environment, and on and on in an escalating evolutionary arms race with little room for compromise. A new paper published in eLife from the lab of Harmit Malik, a professor in the Basic Sciences Division at Fred Hutch, examines the evolutionary strategies that host species use to strike back against colonization by harmful parasites.

The yeast Saccharomyces cerevisiae has, for millions of years, played host to the 2µ plasmid, a parasitic selfish genetic element (SGE) that co-opts the yeast cell’s molecular machinery to promote its own replication and transmission to its hosts progeny. Dr. Malik’s research team, led by graduate student Michelle Hays, hypothesized that some natural yeast strains likely evolved to resist infection by the 2µ plasmid, and this host-parasite relationship presented a good opportunity to better understand the evolutionary battle waged between parasite and host. “It is often difficult to study natural variation in resistance, because hosts and/or parasites are often intractable in the laboratory. Budding yeast provide an ideal system to study host-SGE genetic conflicts”, they explain. Yet even in this ideal system, identifying the genetic basis of evolution required an innovative new technical approach. “To determine if there is heritable natural variation in 2µ plasmid stability in S. cerevisiae strains, we needed an assay to measure plasmid maintenance at the single-cell level…We therefore designed a high throughput assay using a reporter 2µ plasmid.” The new assay, called SCAMPR (Single-Cell Assay for Measuring Plasmid Retention), employed a 2µ plasmid genetically engineered by the group to express GFP. Because 2µ plasmids exist in yeast cells in multiple copies, and GFP florescence scales with plasmid copy number, the team could use flow cytometry to infer the parasitic burden of millions of individual cells and correlate this phenotype with genetic information to identify the mutations that provide yeast with resistance to parasitic infection.

Using the SCAMPR technique, the team examined 52 natural yeast isolates to find strains that could fight back against infection by the modified GFP-2µ plasmid. One such strain, Y9, was able to destabilize the plasmid during mitosis, rendering it strongly resistant to the parasite. This capability was dominant and heritable, indicating it was an evolved trait whose genetic origin could be tracked down. To identify the mutation responsible for this resistance, they performed quantitative trait locus (QTL) mapping on outcrossed Y9 strains to find the region of DNA which consistently segregated with plasmid resistance. This experiment identified that a mutation in MMS21, an essential SUMO E3 ligase involved in mitotic chromosome segregation, is partially responsible for 2µ plasmid resistance, likely via destabilization of the plasmid during mitosis.

This work beautifully illustrated the power of this system to identify the genetic mechanisms of host-parasite coevolution, but it is just the beginning of a larger plan that Dr. Hays, who recently started a postdoc with Dr. Gavin Sherlock at Stanford, has for this system. “[The 2µ plasmid] was popular in the ‘80s for studying replication and for building molecular tools, but I think the natural 2µ plasmid is ready to see a second heyday as a model parasite”, she said. “[In my postdoc] I’ll be using experimental evolution approaches to explore the ramifications of genetic conflict in yeast. I'm excited to explore not just was HAS happened in natural populations, but also what CAN happen under specific conflict pressure in the lab.”

yeast colonies expressing the GFP-2u plasmid
Yeast Colonies (brightfield, left) infected with the GFP-2µ plasmid (GFP, right).

Hays M, Young JM, Levan PF, Malik HS. A natural variant of the essential host gene MMS21 restricts the parasitic 2-micron plasmid in Saccharomyces cerevisiae. Elife. 2020 Oct 16;9:e62337. doi: 10.7554/eLife.62337.

This work was supported by an NSF graduate research fellowship (DGE-1256082 to M.H.), NIH/NHGRI Genome Training Grant at the University of Washington (5T32HG000035-20 to M.H.), NIH R01 grant (GM074108 to H.S.M.) and an Investigator award from HHMI (to H.S.M.).

Fred Hutch/UW Cancer Consortium member Harmit Malik contributed to this work.