CAREER Awardee to Explore How New Genes Emerge and Gain New Functions

Some fish survive in seawater so cold it would freeze the body fluids of most animals. They do it with the help of antifreeze proteins, tiny molecules that help keep ice crystals from forming in their bodies. 

For Xuan Zhuang, an assistant professor of biological sciences at the University of Arkansas, those ice-defying proteins are a window into one of biology's most fundamental questions: How do these new genes arise, gain useful functions and help organisms adapt to harsh environments? The National Science Foundation has awarded Zhuang $1.3 million through its Faculty Early Career Development Program, known as a CAREER Award, to investigate that question. 

The project will focus on Type 1 antifreeze proteins, known as AFPI, found in four distantly related fish lineages: flounder, sculpin, cunner and snailfish. Although the proteins have similar sequences and do the same job, they appear to have evolved independently. That makes them a natural test case for convergent evolution, in which different species arrive at similar solutions through different genetic routes. 

"We want to know where new genes come from, how they evolve and how they gain new functions," Zhuang said. The four fish groups give her team a rare opportunity to compare species that solved the same survival problem more than once. 

Zhuang's team will compare fish species that have AFPI genes with close relatives that do not. The researchers will search for DNA sequences that may have served as starting material for new genes, examine when and where those genes are turned on, and map the genetic "switches" that help a new gene become part of a larger biological network. They will also study how natural selection shaped whether AFPI genes were expanded, kept, altered, disabled or lost as environments changed. 

The work builds on previous research from Zhuang's lab showing that new genes can form by repurposing fragments of older genes while also incorporating newly evolved coding regions, the parts of DNA that carry instructions for making proteins. The CAREER Award will enable her lab to broaden that work from gene birth to gene success: how a new gene becomes regulated, connected to other genes and useful to an organism. 

Zhuang said the project addresses a major gap between finding a gene sequence and understanding what that sequence does. "To link the sequence to a function is a big gap," she said. The expected result is a broader framework for understanding how genomes generate new functions, with relevance beyond antifreeze proteins to other adaptive traits and to fields such as biotechnology and data-intensive biology. 

The award also includes education and outreach components. Zhuang will bring hands-on evolution activities to K-12 students and families in Arkansas through annual museum events. She will also bring project-generated datasets into classroom research experiences for college students, giving them practice with real biological data from genomics and cutting-edge fields. 

CAREER awards are the NSF's most prestigious award for early career faculty who have the potential to serve as academic role models in research and education and to lead advances in their department or organization. The awards are for five years and include teaching and public-outreach components. This award will help cement the foundation of Zhuang's career.