Probing a mystery of evolution

It’s a monumental project, executed by an unlikely team.

With a group of high school scientists, William Duax, a professor of structural biology, is probing one of evolution’s greatest mysteries: Which life form—or life forms—preceded all others on Earth. The researchers are looking for clues in the ribosome, a piece of biological machinery that every living thing possesses.

The project stands out for two reasons.

First, the team’s methodology is unique. Duax believes that the ribosome holds clues to more than 3 billion years of evolutionary history and he has designed a search tool to mine the genomes of more than 7,000 species for these leads.

Second, the decision to engage high schoolers in such high-level work is unusual. The laboratory includes teenagers from schools across the Buffalo-Niagara region, including many from City Honors School in Buffalo. These are the co-authors whose names will appear alongside Duax’s in any peer-reviewed journal articles the endeavor produces.

Duax, a research scientist at the Hauptman-Woodward Medical Research Institute, has published more than 275 scientific papers and served as president of the International Union of Crystallography. He worked closely for many years with the late Herbert Hauptman, the Nobel Prize-winning mathematician whom Duax helped recruit to HWI in the 1970s.

At this point in his career, Duax would like to pass his love of science on to a new generation, and training teenagers to hunt for the first life on Earth is one way to achieve that.

“The most gratifying aspect of the project is working with wonderful Buffalo high school students and watching them become passionate about basic research,” Duax says.

Ribosomes are the part of the cell responsible for synthesizing protein in the body. Perhaps because of the importance of the task, the structure of the proteins that makes up the ribosome itself has changed little over the course of history.

Changes in ribosomal proteins are so rare, in fact, that Duax believes it’s possible to trace the course of evolutionary history through deviations.

Duax and his young colleagues are comparing the makeup of ribosomal proteins in different organisms. To do this, they have developed a method for aligning the genetic sequences of ribosomal proteins across species in every kingdom of life, Duax says.

Here’s how it works: Every protein consists of a chain of amino acids, and the amino acids that sit where each protein twists and folds are highly conserved across species. Using these amino acids as benchmarks, the student-scientists are able to align and compare the amino acid and genetic sequences of ribosomal proteins from many different organisms.

The research has uncovered some extraordinary patterns.

In a ribosomal protein called S19, a single change in the sequence of amino acids forming the protein had intriguing implications. When the researchers looked at S19 in several thousand bacteria, eukaryotes and archaea, they found that changing an aspartic acid to an asparagine in a single position was enough to separate nearly all gram-positive bacteria from all the other species, including gram-negative bacteria.

Ninety-five percent of gram-positive bacteria had an aspartic acid at the designated location, while 95 percent of gram-negative bacteria—along with eukaryotes and archaea—had the asparagine, according to a research abstract Duax presented as part of the 2011 Albany Conversation, a conference on proteins. This suggests, in keeping with common wisdom, that gram-positive bacteria, which have a single cell membrane, preceded gram-positive bacteria, which have two, in the course of evolution.

Duax says this and other evidence points to actinobacteria as the ancestor of all other species.

Charles Carter Jr., a professor of biochemistry and biophysics at the University of North Carolina-Chapel Hill, says the work that Duax is doing on ribosomal proteins holds promise. “I believe that what he’s found is important, and that other people should be paying attention to it,” Carter said after reading the Albany Conversation research abstract.

Carter, who worked with Duax about a decade ago to study the origins of aminoacyl-tRNA synthetases, which facilitate protein translation, believes it is crucial for scientists to explore unconventional ideas. To gain acceptance in the scientific community and publish the results in a peer-reviewed journal, Duax will need to corroborate his results with other kinds of evidence, Carter says.

The work that Duax is doing is off the beaten path, but that’s part of why he finds it exciting. After half a century as a professional scientist, he still finds beauty in the mysteries of life—and the science that can help solve them.

“I’m interested in the underlying reality of the world around us,” Duax says. “We are developing methods by which families of proteins can be aligned perfectly. Colleagues are stunned by the beauty of the alignments. Although our results question some past assumptions and current theories, the results are consistent with most reliable evidence concerning species evolution and function, and point the way to a better and more detailed understanding of 3 billion years of evolution of life.”

The importance of pursuing unusual lines of inquiry is a lesson Duax learned from Hauptman. In the 1950s, Hauptman and a colleague came up with a method for discerning the shapes of different molecules, identifying the precise position of every atom.

The finding was revolutionary and would win Hauptman and his partner a Nobel Prize decades later. But at the time of the discovery, few people in the scientific community accepted his ideas. 

“When he proposed doing what he said he would try to do, almost without exception the entire community said that wasn't possible,” Duax says. “Those of us who knew him lived through that period. We saw him explain his work to people, saw him get rejected and saw him persevere.”

“He never got upset,” Duax remembers. “He just persevered—because the data suggested to him that it could be done.”