Build-a-Genome (BAG) course 

Boeke studied transposable elements in yeast and mammalian cells. Along the way, he decided to synthesize transposon DNA from scratch. “I was impressed with the power of being able to do that, which led me to synthesize first a synthetic chromosome arm and eventually the entire yeast genome with people around the world,” he describes. Using this first synthetic eukaryotic genome project, Boeke developed a unique laboratory component for his class that allowed students to contribute to this mammoth research endeavor.

“We built the genome from scratch, starting with oligonucleotides to entire genomes worth of synthetic chromosomes, piece by piece. In the early phases, we involved a lot of undergraduate students,” he explains. For Boeke, the course had two essential components. “One was to use the manpower needed to build such an enormous genome. The other was that it’s a fantastic way to teach molecular biology and genetics to undergraduate students, for whom it was new. They were doing original research as part of a course, learning about how to do a PCR reaction,” he shares. Because students were synthesizing genome fragments that were never created before, they faced several setbacks and performed extensive troubleshooting. This integral component of the course provided an authentic research experience to students.

Eventually, the course evolved as the technologies advanced. In the early years, students would generate 750 base pairs (bp) of synthetic fragments using PCR reactions on overlapping oligos. They would run gels to get clean bands and regularly present their observations in lab meetings. However, as the cost of synthesizing synthetic DNA fragments rapidly decreased, the course shifted from fundamental molecular biology in E. coli to yeast genetics. “The students started assembling medium-sized DNA pieces into bigger pieces using homologous recombination in yeast. After successfully running the course for 20 years and using work from undergraduate students, they are now helping combine sixteen fully man-made synthetic chromosomes and put them into a single strain,” says Boeke.

“Running the course wasn’t always easy,” describes Patrick Cai, Professor of Synthetic Genomics at the Manchester Institute of Biotechnology and former course instructor. “Boeke was running the course on a very limited budget, so we did a lot of work ourselves. One night, he drove his pickup truck and two of us moved all the chairs across the campus to a new course location. He was that dedicated and serious about the course,” says Cai.

With Boeke’s steadfast commitment and exceptional planning, the course eventually culminated in a global research and teaching consortium. Researchers from across the globe came to Boeke’s laboratory and learned teaching modules to build their parallel courses. “For example, Yingjin Yuan, Professor of Biochemical Engineering at Tianjin University, came to us and we helped him set up this course in China. He and colleagues focused on turning the course into a production machine and developed a landmark project by finishing one whole synthetic yeast chromosome in just a year,” says Boeke.

Teaching how to teach

Boeke involved his graduate students and postdoctoral researchers in teaching the course. According to Lisa Scheifele, Associate Professor in the Department of Biology at Loyola University Maryland, “The number of postdoctoral fellows and graduate students who have been empowered to learn the art of teaching, mentoring students, and developing course structure and content is notable and impressive.” She adds, “Boeke has been incredibly supportive of trainees who wanted to include a significant teaching aspect in their future careers. The Build-a-Genome course was my first teaching experience that ‘lit the fire’ for a future career where I’ve been able to blend teaching and cutting-edge research as we have done in Build-a-Genome.” Plus, the fact that this course inspired several of Boeke’s trainees in pivoting to a teaching career is something he’s quite proud of.

Harnessing the power of designer yeast

The synthetic yeast genome built through this innovative laboratory course offered a major paradigm shift in genetics and biotechnology, showcasing how to design and assemble synthetic DNA at scale. These synthetic chromosomes further facilitate testing genome fundamentals traditionally difficult to dissect in laboratory yeast strains. “Our knowledge about yeast genetics is largely based on our observation of the natural yeast genomes, which sometimes can be difficult to study. The synthetic yeast genome allows us to engineer the genomes to address societal challenges,” explains Cai. For example, Boeke made a bold choice to remove all the tRNA genes from the synthetic chromosomes and put them all on a new chromosome, allowing researchers to engineer it independently of all the other chromosomes. Now, Cai is testing yeast strains with tRNAs adapted to human codon usage to better express human proteins that can in turn be used in therapeutic applications to increase product yield.

Join us in congratulating Jef Boeke, who received the Elizabeth W. Jones Award for Excellence in Education, on behalf of Build-A-Genome, at The Allied Genetics Conference 2024 in Metro Washington, DC. And congratulations to the Build-a-Genome team whose members include Jessica Dymond of In-Q-Tel; Lisa Z. Scheifele of Loyola University Maryland; Eric Cooper of Hartwick College; Robert Newman of North Carolina Agricultural and Technical State University; Franziska Sandmeier of Colorado State University, Pueblo; Yu (Jeremy) Zhao of NYU Langone Health; Stephanie Lauer of St. Thomas Aquinas College; and Raquel Ordoñez of NYU Langone Health.

2024 GSA Awards Seminar Series

In a recent seminar, Jef Boeke, who received this award on behalf of Build-a-Genome, described how the course teaches students fundamental principles of genetics and how to perform, interpret, and troubleshoot an experiment when the outcome is unknown. He also touched on the history of the course and the resultant Network of Build-a-Genome courses, how it has affected students and instructors, and the course’s impact on the overarching International Sc2.0 project. Watch the recording here.

Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

While Riddhiman Garge, first author of a study published in the March 2024 issue of G3: Genes|Genomes|Genetics, was earning his PhD at the University of Texas, he met brewer Chip McElroy. McElroy, who owns Live Oak Brewing Company and has a Ph.D. in biochemistry, was curious about what happens to brewing yeast inside fermentation tanks. The pair teamed up with Garge’s colleagues to investigate some aspects of this question.

The importance of brewing yeast

In addition to being a classic research organism for genetics and molecular biology, Saccharomyces cerevisiae, sometimes called brewer’s yeast, has a host of commercial uses and is especially important in beverage fermentation—the global beer market is now worth more than $750 billion.

Despite its economic impact, however, brewer’s yeast has been understudied in its beer-making context. The G3 study investigates one aspect of commercial fermentation: how ale yeast proteins change throughout successive fermentations.

The impact of serial repitching on the yeast proteome

During brewing and fermentation, yeast must adapt to increasingly harsh conditions, including fluctuating nutrient, ethanol, and oxygen levels. (Indeed, too much alcohol stresses both yeast and humans!) The commercial practice of serial repitching may also impact the yeast proteome.

In serial repitching, brewers harvest yeast cells at the end of a fermentation cycle and use them to inoculate (or pitch) a new batch of beer. Commercial brewers repitch eight to ten times, stopping as the flavor, aroma, and yeast viability deteriorate over time.

To better understand molecular changes associated with serial repitching, researchers sampled populations of Weihenstephan Wheat yeast directly from the fermentation tank. They applied shotgun mass spectrometry to measure proteomic changes throughout two fermentation cycles separated by fourteen rounds of serial repitching. The time course began with Batch 1—the freshly prepared yeast stock—and ended after fourteen repitches (Batch 15), and sampling was performed at comparable time points across the four days of brewing.

Results

Garge et al. report that protein abundance at the earliest fermentation timepoints was the most different compared to the rest of the timepoints. Batch 15 had elevated synthesis enzymes for ergosterol, which helps mitigate the stress of low-oxygen environments; however, batch 15 had fewer isobutyraldehyde synthesis enzymes. Isobutyraldehyde is linked to a grainy flavor profile that is considered desirable for some beers but an off-flavor in others. This dataset offers a starting point for tweaking flavor and strain characteristics in commercial and craft breweries.

The authors also set up an interactive web interface cataloging the fermentation-based protein changes they observed to aid hobbyists, scientists, and brewers. 

Next steps

Further analysis of the study data and future studies of proteins and metabolite changes across fermentation and repitching will help brewers engineer yeast strains, optimize brewing workflows, and study trends that undergird domestication processes. In addition, such real-world research can help make inferences about known and unknown biology. For instance, the function of many S. cerevisiae genes is unknown. “By looking at [these genes] in new contexts, maybe we can infer function,” Garge says. “People think that if you have a biology degree, you can only study things in the lab. But this study [demonstrates] that there are interesting biological processes going on in the everyday world,” Garge says.

Don’t miss the opportunity to hear these outstanding scientists discuss their work. Access the full conference schedule online.

C. elegans 

Sydney Brenner Award

Sneha Ray 

Fred Hutchinson Cancer Research Center  

The Sydney Brenner Dissertation Thesis Award is presented to a graduate student who has completed an outstanding PhD research project in the area of genetics and genomics of C. elegans.

Drosophila 

Larry Sandler Award

Sherzod Tokamov

University of California, Berkeley

The Larry Sandler Award is presented to outstanding recent graduates who have completed a PhD in an area of Drosophila research. The award serves to honor Dr. Sandler for his many contributions to Drosophila genetics and his exceptional dedication to the training of Drosophila biologists. 

Mammalian 

IMGS President’s Award

Jason Bubier

The Jackson Laboratory for Mammalian Genetics

This new award, the IMGS President’s Award, is presented to an early career scientist in recognition of their exceptional accomplishments in independent research in mammalian genetics. The award celebrates their contributions both to the IMGS and the field of genetics as a whole.

Population, Evolutionary and Quantitative Genetics (PEQG) 

James F. Crow Early Career Researcher Award

Olivia Harringmeyer

Harvard University

The James F. Crow Early Career Researcher Award is presented to students and recent PhDs conducting PEQG research. The award serves to honor Professor James F. Crow and his numerous, impactful contributions to the field of genetics. 

Yeast 

Angelika Amon Award

Xiaoxue Snow Zhou 

New York University

The Angelika Amon Award is presented to an outstanding recent PhD graduate. The award serves to honor Dr. Amon for her many discoveries through the use of yeast genetics, and her exceptional dedication to training and mentorship.

Zebrafish 

International Zebrafish Society Genetics Trainee Award

Mollie Sweeny 

Duke University 

The International Zebrafish Society Genetics Trainee Award recognizes excellence in research, in particular discoveries leading to significant scientific or technological advances through the use of zebrafish genetics.

GSA is pleased to announce the recipients of the DeLill Nasser Award for Professional Development in Genetics for Spring 2022! Given twice a year to graduate students and postdoctoral researchers, DeLill Nasser Awards support attendance at meetings and laboratory courses.

The award is named in honor of DeLill Nasser, a long-time GSA supporter and National Science Foundation Program Director in Eukaryotic Genetics. Nasser was regarded by some as the “patron saint of real genetics,” shaping the field through more than two decades of leadership. She was especially supportive of young scientists, people who were beginning their careers, and those trying to open new areas of genetic inquiry. For more about Nasser, please see the tribute from Scott Hawley, published in the August 2001 issue of GENETICS.

Jon Hibshman

Postdoctoral fellow, University of North Carolina, Chapel Hill

“My research seeks to understand how some animals can survive extreme stresses like desiccation.”

Diedre Reitz

Postdoctoral fellow, University of California, Davis

“My research aims to understand the mechanisms responsible for preventing homologous recombination-mediated genome rearrangements between repetitive elements.”

Anna Moyer

Postdoctoral fellow, University of Alabama, Birmingham

“I use zebrafish to understand how the overexpression of chromosome 21 genes contributes to abnormal brain development in people with Down syndrome.”

Jennifer Chik

Postdoctoral fellow, University of California, San Diego

“My research focuses on identifying and characterizing multi-functional proteins with roles in two critical pathways: amino acid metabolism and chromatin regulation.”

Shannon Hateley

Postdoctoral fellow, Carnegie Institution for Science

“I use computational biology and ecological genomics methods to investigate how plants will adapt to climate change.”

Maria Sterrett

PhD candidate, Emory University

“We study human disease mutations that impact conserved RNA regulatory pathways by modeling the mutations in yeast and assessing the functional and molecular consequences using genetics and biochemistry techniques.”

Emily Hendricks

Master’s student, Southern Illinois University, Edwardsville

“My research uses Drosophila to study the molecular mechanisms of synaptic dysregulation in neurodevelopmental and neurodegenerative diseases.”

Uzezi Okinedo

PhD candidate, University of Massachusetts, Boston

“I study the genetic basis of adaptation in African rice (Oryza glaberrima) to identify and characterize domestication loci for potential genetic improvement.”

Sophia Sanchez

PhD candidate, University of Texas, Austin

“We leverage C. elegans to understand the individual contribution of Hsa21 genes to cellular and molecular phenotypes that could be important in Down syndrome.”

Vladimir Lazetic

Postdoctoral fellow, University of California, San Diego

“My research focuses on uncovering novel mechanisms that regulate an immune response against viral and fungal pathogens.”

Yeast screens explore the therapeutic potential of chemical rescue.

Anyone who’s worked in a lab knows that sinking feeling of discovering that the temperature of an incubator, carefully set the night before, has crept up high enough to ruin the experiment. While such a mishap usually spells disaster, occasionally, it can lead to an unexpected discovery.

One such revelation was prompted by an uncooperative incubator in the lab of Michael McMurray, a cell biologist at University of Colorado’s Anschutz Medical Campus. McMurray studies the septin family of cytoskeletal proteins, and inside the incubator were plates of yeast with temperature-sensitive septin mutations. The mutant yeast could survive only at mild temperatures, so the incubator was set to a comfortable 27°C.

For this experiment, a chemical called guanidine hydrochloride had been added to some of the plates, to test whether it would stop the mutants from growing at the permissive temperature. When the incubator was found roasting away at more than 30°C, however, all of the yeast should have been dead.

“Amazingly, one of the mutants actually grew,” says McMurray. “The guanidine restored its viability.”

That discovery launched an investigation of how, exactly, guanidine had protected the mutant from normally lethal conditions. In a paper in the September issue of G3: Genes|Genomes|Genetics, Hassell et al. report several mutants that can be rescued by guanidine. They also show that another naturally occurring small molecule can correct an even broader range of mutants.

Guanidine can stand in for a lost arginine

Guanidine’s molecular structure mimics the side chain of the amino acid arginine. Researchers had previously shown that guanidine could restore function to an enzyme that had been mutated to lack an arginine in its active site. But all of this work had been done in vitro. This piqued McMurray’s interest even more. “Arginine is the most commonly mutated amino acid in human disease,” he says. “If guanidine can restore function to arginine mutant proteins, why has no one explored this in living cells?”

McMurray’s team began by testing enzymes in which a single arginine mutation disabled the enzyme enough to cause disease, such as ornithine transcarbamylase (OTC). OTC deficiency is an inherited metabolic disease that leads to a buildup of toxic ammonia in the body. The researchers created yeast with the same OTC arginine mutation that causes the human disease, making the yeast unable to grow without nutritional supplementation. Adding guanidine hydrochloride to the growth media restored some of the lost enzyme function.

“The effect was pretty small,” McMurray says. “It wasn’t a full rescue, but it was something.”

Next, the researchers decided to broaden their investigation. Instead of testing candidate enzymes, they screened hundreds of yeast mutants to see if guanidine restored function to any of them. “We decided to let the cells tell us what would work best,” McMurray says. “That’s when things started to get interesting.”

The screen uncovered 11 new candidates, the most interesting of which was an arginine mutant of actin, another cytoskeletal protein. “It just so happens that arginine is also mutated in human cardiac beta actin, and that mutation causes disease,” McMurray says.

As an ATPase, actin is technically an enzyme, but the arginine mutation is far from the active site, and guanidine isn’t restoring catalytic activity per se. Instead, McMurray says, it’s helping the protein fold into its proper 3D shape. “All proteins have to fold,” McMurray says. Protein folding results from chemical interactions between the side chains of various amino acids. “To rescue the mutant, the guanidine just has to be able to fix what’s missing and restore the folding.”

The idea of rescuing mutants by restoring proper protein folding led them to investigate other chemicals that can influence protein folding. “From a biological perspective, what are other cases in nature in which organisms have to deal with alterations in protein folding?” McMurray says. “Then we thought of sea creatures — sharks and rays.”

Moving beyond guanidine

Because they live in saltwater, sharks maintain high concentrations of urea in their bodies to keep from losing water through osmosis. Urea, however, is toxic to proteins, and causes them to unfold. To counteract the urea, these animals also have high levels of a chemical called trimethylamine oxide (TMAO), which promotes protein folding.

Does the shark’s protein protection trick work in other contexts? To follow up, research assistant Daniel Hassell screened yeast mutants using TMAO. He turned up hundreds of mutants that were rescued by the molecule. The genes and mutant types were all very different from each other, suggesting that TMAO has a more general stabilizing effect rather than specifically replacing a particular amino acid. This broad effect suggests a potential role for the molecule in synthetic biology, as a way to design proteins with an on/off switch system.

For its part, guanidine is already FDA-approved as a treatment for an inherited autoimmune disorder called Lambert-Eaton myasthenic syndrome. McMurray remains curious about whether it has the potential to treat other genetic diseases.

“That would be my ultimate hope, that someone would be inspired by our work to try it in an animal model or the clinic,” McMurray says.

CITATION

Chemical rescue of mutant proteins in living Saccharomyces cerevisiae cells by naturally occurring small molecules
Daniel S Hassell, Marc G Steingeisser, Ashley S Denney, Courtney R Johnson, Michael A McMurray
G3 Genes|Genomes|Genetics 2021; jkab252
https://doi.org/10.1093/g3journal/jkab252

Discovery of thiabendazole target explains vascular disrupting action.

Even after hundreds of millions of years of evolution, some yeast genes persist mostly intact in humans and other vertebrates. Despite the huge differences between yeast and humans, these genes perform the same molecular function in both organisms but have been adapted over time into new contexts. Learning about these evolutionarily enduring genes can provide important insight into complex systems in large organisms.

About a decade ago, researchers led by molecular biologist Edward Marcotte and John Wallingford of the University of Texas at Austin discovered that a medication used to treat fungal infections and ringworm could also stop new blood vessel formation in vertebrates. The drug, called thiabendazole (TBZ), would even cause recently formed blood vessels to break apart and dissolve. Although TBZ had been in clinical use for decades, nobody knew exactly how the drug worked at the molecular level.

Now, in a new paper in GENETICS, Marcotte and colleagues have identified the molecular target of TBZ’s blood vessel-disrupting action. It’s called beta-tubulin 8, or TUBB8, a structural protein that helps provide the cell’s skeletal system. The discovery explains why TBZ kills fungi but not vertebrates.

Studying human genes in yeast

The story began with the realization that certain interacting networks of genes needed for survival in single-celled organisms like yeast had survived billions of years of evolution and remained active in vertebrates, including humans. 

“They’re inherited intact as a system,” Marcotte explains. As new organisms emerged through evolutionary processes, they developed different body plans and ecological niches. During these changes, many gene networks continued working together, but were recruited to different systems in different organisms. 

“In yeast, they get wired up to do one thing, and ultimately in the vertebrate lineage they get wired up to do something else,” Marcotte says. “That’s the kind of process we’re talking about.”

Studying these networks revealed that a set of genes that keep the yeast cell wall intact also help blood vessels grow properly in vertebrates. This led to the discovery that TBZ could stop blood vessel formation.

“That discovery got us really intrigued about the extent that human and yeast genes were still doing the same thing,” says Marcotte. “Questions like that made us wonder how much yeast and human genes were still equivalent.”

To study the questions, the researchers created strains of yeast in which they substituted the original yeast gene with its human counterpart. In cases where the human gene adequately sufficed for the lost yeast gene, the “humanized” strain of yeast became a valuable research tool. They successfully created several hundred of these strains.

“What’s great about yeast is that we can study human genes in a simplified context,” says Riddhiman Garge, the paper’s co-first author, who is now a postdoctoral fellow at the University of Washington and performed the work collaboratively with researcher Hye Ji Cha.

Tracing the tubulin family tree

TBZ, they knew, killed yeast by disrupting a structural protein called beta-tubulin. While yeast have one beta-tubulin gene, humans have accumulated nine versions of the gene, and two of them can substitute for the yeast gene. 

“We used molecular modeling to build models of the yeast beta-tubulin and the various beta-tubulins in humans,” Marcotte says. Using these computer models, they simulated interactions between TBZ and each tubulin.

“Out of the nine beta-tubulins, only one looked like it would actually be responsive to the drug,” says Marcotte. 

Over the course of evolution, the one beta-tubulin ancestral gene had been copied and changed until humans had 9 beta-tubulins. Eight of them contain naturally occurring mutations that confer resistance to TBZ. The one that doesn’t, TUBB8, is expressed in blood vessels.

“Thiabendazole doesn’t kill humans, like it does fungus and nematodes, because most human cells have resistant forms of tubulin,” Marcotte says. “It’s known to have a very good safety profile over the decades of use. This result explains why that’s the case, but also explains why it turns out to be active in just a particular tissue in human.”

Potentially, TBZ could be used to treat diseases in which abnormal blood vessel growth is a problem, such as hemangiomas, which are bright red rubbery lumps on the skin made up of excess blood vessels that grow in a cluster. Cancers also tend to spur new blood vessel formation to feed the energy needs of a fast-growing tumor.

Libraries of yeast strains containing human genes can also be used to identify other genetic interactions, or screen for other drugs that have tissue-specific functions in humans.

“I truly believe this is just scratching the surface,” says Garge. “I would love to see more of the community leverage such systems-wide comparisons to gain insights into human health.”

CITATION

Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast

Riddhiman K Garge,  Hye Ji Cha,  Chanjae Lee,  Jimmy D Gollihar,  Aashiq H Kachroo, John B Wallingford,  Edward M Marcotte

GENETICS 2021, iyab101, https://doi.org/10.1093/genetics/iyab101

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.

Register for Award Seminar

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.

Yeast circumvent Dollo’s Law and reacquire traits lost tens of millions of years ago from distant relatives.

Dollo’s Law, first proposed in the 19^th century, holds that evolutionary losses are irreversible — if a species discards a complex trait, it will never reacquire exactly that trait.

However, a study published in Genetics highlighted one way that unicellular fungi can break Dollo’s Law: horizontal gene transfer. Although budding yeasts do not normally mate with distant relatives, data indicate that they can occasionally exchange genetic material and thereby regain lost genes or even gene clusters, despite functioning without them for millions of years.

Odd species out

“Laws in biology are almost meant to be violated. It’s a science of exceptions,” says Chris Todd Hittinger, one of the senior authors. Hittinger leads a laboratory at the University of Wisconsin-Madison, where he and his team study yeast metabolism, biodiversity, evolution, and ecology. This recent study emerged from data observations collected as part of the Y1000+ Project, a National Science Foundation-funded collaboration between Hittinger’s lab, Antonis Rokas’ lab, and others worldwide. The initiative is aimed at cataloging and analyzing genomic and metabolic data for all known yeast species from the subphylum Saccharomycotina in order to understand their evolution and ecological functions.

First author Max Hasse, who was an undergraduate researcher in Hittinger’s lab at the time, was the first to notice something odd in the Y1000+ Project data: some species that feed on the sugar galactose are deeply embedded in clades in which the other species generally cannot use galactose.

“His instincts were absolutely right,” says Hittinger. “For a junior in college to have that kind of scientific insight and know where to follow things really bodes well for his career.”

The researchers investigated the genomic data further and found that in these out-of-place species, the structures of the GAL gene clusters (needed for metabolizing galactose) were strikingly similar to those of distantly related budding yeasts, specifically species in the CUG-Ser1 clade. Further investigation led them to conclude that by far the most likely explanation was that CUG-Ser1 yeast served as common donors of the GAL gene cluster to at least four other species via horizontal gene transfer.

The researchers were somewhat surprised to find horizontal gene transfer in the yeast galactose utilization pathway because Saccharomyces cerevisiae — the best-known model yeast species — has a galactose utilization pathway that is encoded in multiple places throughout the genome, making transfers more difficult. These genes are tightly controlled by dedicated regulatory genes scattered across the genome. However, in CUG-Ser1 yeast, the GALgenes are clustered together and more loosely regulated by conserved factors.

Broader evolutionary takeaways

Although trait reacquisition via horizontal gene transfer is much more common in bacteria and unicellular eukaryotes in direct contact with their environment, this study underscores some broad evolutionary principles that hold true even in multicellular eukaryotes.

“Sometimes in the popular press, evolution gets portrayed as being all about chance,” says Hittinger. “There’s an element of that, but there’s also an element of predictability.” In the case of yeasts, evolutionary trait reconstruction modeling revealed that allowing trait reacquisition in some cases is more evolutionarily likely than only allowing for trait loss across all scenarios. 

However, says Hittinger, “it is still true to a point that once you lose something it’s very hard to regain it.” In the paper, the authors point out that the GAL genes of the CUG-Ser1 clade represent something of a “best-case scenario” for trait reacquisition. This is true for several reasons. As well as the genes being closely collocated and regulated by conserved factors, the phenotype offers a clear competitive advantage in galactose-rich environments, making it more likely that the trait will persist in the species once reacquired.

Even among budding yeasts, trait reacquisition is probably rare in the absence of these factors. The species that reacquired galactose utilization stood out in this study precisely because the vast majority of closely related species had not reacquired the trait, instead continuing down apparently loss-permanent evolutionary pathways.

Next Steps

As the Y1000+ Project continues, “there are a lot of exciting directions,” says Hittinger. In the immediate future, the team intends to follow up on other possible cases of horizontal gene transfer between yeast species, tying the known examples to other losses of metabolic pathways and reacquisitions. “There are lots of great candidates out there.”

CITATION:

Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss

Max A B Haase, Jacek Kominek, Dana A Opulente, Xing-Xing Shen, Abigail L LaBella, Xiaofan Zhou, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P Kurtzman, Antonis Rokas, Chris Todd Hittinger

GENETICS 2021 217: iyaa012. 

https://doi.org/10.1093/genetics/iyaa012

We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our 2020 early career scientist advocates.

Jacob L. Steenwyk
Communications & Outreach Subcommittee
Howard Hughes Medical Institute James H. Gilliam Fellow
Biological Science Department, Vanderbilt University, Nashville, TN

Research Interest

Broadly, I am interested in understanding the tempo and modes of evolution. Understanding these processes in diverse systems can help us address some of the greatest biological mysteries and challenges. For example, why are some microbes deadly pathogens while others are relatively harmless or even beneficial to human affairs?

To address these and other questions, I have three main research projects: (1) understanding the genomic consequences of losing DNA repair genes in an ancient lineage of budding yeasts, (2) examining the genomic and functional outcome of hybridization in a lineage of pathogenic filamentous fungi, and (3) developing methods and tools that help infer and understand the tree of life.

Other projects I have led include examining signatures of rapid evolution in yeast used for wine-making and unraveling the evolutionary history of biotechnologically and medically relevant filamentous fungi.

To date, nearly all of my work has been focused on organisms from the fungal kingdom. In the future, I hope to expand my work to other branches in the tree of life.

As a PhD-trained scientist, you have many career options. What career paths interest you the most?

I hope to become a research professor at a top-tier research institution in the United States. I believe I will be able to establish and carry out an ambitious research program studying rapid evolution across the tree of life as well as the functional genomics of microbial pathogens.

While doing so, I plan to provide a positive mentoring experience for trainees. I have experienced excellent mentorship from my mentors Antonis Rokas (PhD thesis advisor) and John G. Gibbons (Master’s thesis advisor), who have advocated and supported me in numerous ways. I value and appreciate their efforts to help me grow as a scientist and member of the scientific community, and I want to pass on these positive experiences as a mentor of equal caliber and class.

 In addition to your research, how else do you want to advance the scientific enterprise?

As a member of the scientific enterprise, I plan on continuing to be an advocate for diversity, equity, and inclusion, participating in community service and outreach, and using science communication as a tool to bridge the gap between scientists and the broader community.

Matters of diversity, equity, and inclusion are near and dear to me, in part because as an underrepresented minority, I have encountered both unjust and inclusive practices. In light of my experience and the experiences that colleagues have shared with me, I plan on continuing to promote and pass on the positive aspects of my experience in the scientific enterprise and beyond. In line with this goal, I am the acting president of the graduate student-led organization Inclusivity in the Biosciences Association, which proudly advocates for diversity and proponents of inclusion. Similarly, I serve as the Inclusion Coordinator for the Evolutionary Studies Initiative at Vanderbilt University.

As an active participant in community service and outreach, I have been vice co-chair and co-chair of MEGAMicrobe, a half-day event in Nashville, TN, that features interactive and informational booths aimed at teaching people ages 6-14 about the wonders of microbes. Additionally, I have participated in multiple art shows and given talks about the intersection of science and art. Two examples of my science-influenced art (sciart) are The Abstract Art of Algorithms and an abstracted portrait of sun-bathing frogs. The latter sciart is an ode to the frogs that have died due to a deadly fungal disease. For more information about my sciart, see a recent interview organized by Kathryn Royster.

Now, I am thrilled to be a co-chair of the Communications & Outreach Subcommittee working alongside great members of the science communication and outreach community at the Genetics Society of America, including my fellow co-chair Angel Fernando Cisneros Caballero, Adelita Mendoza, and many others!

As a leader within the Genetics Society of America, what do you hope to accomplish?

Within the Communications & Outreach Subcommittee, I hope to help foster an inclusive and productive environment and facilitate the subcommittee’s members’ abilities to write and publish popular science articles on topics they are passionate about. I also aim to publish my own popular science articles with fellow subcommittee members.

Many of us have similar goals but entirely unique perspectives that can enrich and inform one another. Beyond the Communications & Outreach Subcommittee, I aim to help build bridges between the different early career subcommittees and other groups within the Genetics Society of America.

Previous Leadership Experience:

2019–Present: Inclusion Coordinator, The Evolutionary Studies Initiative at Vanderbilt, Vanderbilt University, Nashville, TN

2019–Present: President, Inclusivity in Biosciences Association, Vanderbilt University, Nashville, TN

2019–2020: Co-chair, MEGAMicrobe, Vanderbilt Institute for Infections, Immunology and Inflammation, Nashville, TN

2018–2019: Vice President, Graduate Student Association, Department of Biological Sciences, Vanderbilt University, Nashville, TN

2017–2018: Scientific Consultant, Little Harpeth Brewing, Nashville, TN

Keep up with Jacob L. Steenwyk through various social media and other platforms!

• Personal website
• Twitter account
• Google Scholar page
• ResearchGate profile
• LinkedIn profile
• GitHub profile