Failure of chromosomes to segregate properly results in severe medical conditions, or even death. Yet for a long time, it was challenging to study exactly how chromosomes carry out their complex choreography, due to a lack of robust tools for combining chromosome visualization and genetic experiments.
Douglas Koshland spent his postdoc studying mammalian chromosome biology in Marc Kirschner’s lab at UC San Francisco. From that experience, he was inspired to develop a cytological assay to enable the study of chromosomes in baker’s yeast. Working with yeast would provide access to the most sophisticated genetic tools, but tiny yeast chromosomes had thus far been impossible to visualize. “At the time that we started these studies, yeast was about the farthest thing that people would use to study chromosome structure,” Koshland recalls. “It had no cytologically visible chromosome structure.”
Using genetic approaches, Koshland and Alex Strunnikov discovered the SMC family of proteins that were conserved from bacteria to humans and likely played a role in chromosome structure. To test this hypothesis, Koshland convinced Vincent Guacci, a talented postdoc, to develop a fluorescence in situ hybridization method that allowed researchers to visualize differences in yeast chromosome structure in interphase and mitosis. With this new tool, his lab and others discovered that SMC proteins were key subunits of complexes known as “cohesin” and “condensin” that mediate sister chromatid cohesion and condensation in all eukaryotes.
His advances in chromosome biology have not only illuminated fundamental features of the structure of chromosomes, but also provided tools for many others to use. For his achievements, Koshland has been awarded the 2021 Genetics Society of America Medal for outstanding contributions to the field of genetics in the last 15 years. “What Doug likes to do is to find problems that people appreciate are important but hard, then find ways of approaching them,” says Jasper Rine of UC Berkeley, one of the scientists who nominated Koshland for the award. “Doug is a pioneer who opens up the ability to study things that people had not considered approachable.”
The cohesin complex holds the two sister chromatids together after DNA replication, and condensins help pack the DNA into a compact shape. Previously, it had been thought that the helical intertwining of the sister chromatids held the two molecules together until they were untangled by topoisomerases, but that turned out not to be the case. “Doug showed that wasn’t the case at all by clever genetics experiments and also by discovering the proteins that really are responsible,” says Rine. Cohesin proteins hold sister chromatids together, create topologically associated domains, and participate in DNA repair.
“One sort of prophetic thing I got right was to say that given how complicated DNA replication is, there’s no reason to believe higher order chromosome structure is going to be any less complicated.” Koshland recalls. “And this turned out to be true. We’ve spent the last 20-odd years trying to figure out what the dang things do.”
Koshland has continued to pursue complex questions about distinctive chromosome structures by studying them in yeast. For instance, chromosome loops had been observed in mammalian cells, and it was thought that the looping might bring together regulatory elements and the promoters they regulate. “In collaboration with the Darzacq laboratory, we improved the technology for looking at these loops,” Koshland says. “It looks like the looping is just as beautiful in yeast, and very analogous to what you see in mammalian cells.” Yeast don’t generally have distal gene regulatory elements, however, so the function of these yeast chromatin loops, and by extension many mammalian chromatin loops, probably isn’t the regulation of gene expression. With the technology to study the loops in yeast, the power of yeast genetics is now available to establish the physiological relevance of exciting in vitro studies of loops formation, elucidate loop regulation in vivo, and to discover their mysterious biological function.
Another curious chromosomal phenomenon the lab is exploring is the formation of “R-loops,” in which RNA hybridizes back to the DNA it originated from. R-loops cause double-stranded breaks in the DNA, which leads to chromosome instability. Koshland’s lab showed that not only do the R-loops introduce breaks, but they actually interfere with DNA repair. “They both cause the break and then they mess up the repair process,” Koshland says. These structures may be responsible for chromosomal rearrangements seen in cancer cells.
Finally, Koshland’s lab is also studying desiccation tolerance as a window into stress biology. Some organisms, like the resurrection fern, can recover after going through desiccation. Most desiccation tolerant species seemed to have an abundance of two factors: the sugar trehalose and a family of proteins called hydrophilins. Koshland’s group demonstrated that these are both necessary and sufficient for desiccation tolerance. “That was a stunning observation,” Koshland says. Rather than relying on complex, specialized pathways to protect the cell from DNA damage and other effects of stress, all that was needed was a simple sugar and a set of small, intrinsically disordered proteins. “Now the question is understanding exactly how they work,” Koshland says.
Over the years, Koshland has kept his lab on the small side, and as a mentor he is known for his thoughtful manner and intellectual rigor. Plus, “he’s just an incredibly nice person,” says Orna Cohen-Fix of the National Institute of Diabetes and Digestive and Kidney Diseases and a former postdoc in Koshland’s lab.
“When I was starting my own lab, if you asked me at the time who do I want to be when I grow up, I’d say ‘I want to be Doug,’” Cohen-Fix says. “He puts emphasis on getting things right and being thoughtful. It’s more important to him to understand a process than to publish in a high-profile journal.”
Koshland will accept the award and present “Genetics of chromosome biology: to null or not to null” at an online Award Seminar on Tuesday, May 11, at 2 p.m. EDT.
The Genetics Society of America Medal honors an individual member of the Society for outstanding contributions to the field of genetics in the last 15 years. GSA established the Medal in 1981 to recognize members who exemplify the ingenuity of the GSA membership through elegant and highly meaningful contributions to modern genetics.