The Roots of Biodiversity: How Proteins Differ Between Species

To better understand what drives biodiversity on Earth, scientists have historically looked at genetic differences between species. But that only gives part of the picture. The characteristics of a given species are not only the result of its genes, but also of the proteins that those genes code for. Understanding the differences between species’ proteomes — or any proteins that can be expressed — is therefore just as important as understanding the differences between genomes.

In a new study, Yale researchers compared the proteomes of skin cells from 11 mammals, which will help scientists understand the molecular drivers of biodiversity and how these factors evolved over time.

They found that while many proteins are similarly variable both between species and within species, some are more variable between species, providing clues as to which proteins may be more important in mammalian evolution. The work may also help researchers understand why some species are more resistant to cancer.

Their findings were published on September 9th scientific advances.

“To understand biodiversity and how DNA differs between species, you might also want to know how species behave, evolve and look differently,” said Günter Wagner, Alison Richard Emeritus Professor of Ecology and Evolutionary Biology.

And those attributes — how a species looks, behaves, and evolves — are probably more closely related to protein content than DNA, explained Yansheng Liu, an assistant professor of pharmacology at the Yale School of Medicine.

However, comparing protein levels between species was difficult because the technology for large-scale analysis did not yet exist. But Liu has used a method called data-independent acquisition mass spectrometry that now allows researchers to do this type of work.

“It’s a conceptual and technical breakthrough that allows us to work at this higher, more functionally relevant level,” Wagner said.

Liu is a member of the Yale Cancer Biology Institute and Wagner is a member of the Systems Biology Institute, both located on Yale’s West Campus. There their collaboration began during a symposium on cancer systems biology, which they both attended.

For the study, the researchers quantified all of the proteins expressed in skin cells from 11 mammalian species: rabbits, rats, monkeys, humans, sheep, cows, pigs, dogs, cats, horses and opossums.

They found that the analysis provided information that could not be obtained with other techniques. For example, while previous research has looked at differences in mRNA — the genetic material used to make proteins — they found that measuring proteins provided additional information that could not be captured by analyzing mRNA alone, since mRNA is only an indirect measure of protein abundance.

A strand of mRNA carries the code for the formation of a protein. And while individual proteins can have a specific function, proteins can also interact with each other and act as groups, Liu explained. Just looking at the mRNA does not provide this information.

“We found that the protein relationship to mRNA is very low, especially for certain protein classes,” says Liu. “This means that the mRNA profile alone would be misleading.”

The team then looked at protein variation both between species and between individuals of the same species and found that for most proteins, levels that differed more between individuals were also more different between species. But there were some proteins that didn’t fit this trend. For example, proteins associated with cell division and RNA metabolism were more different between species than between individuals of a species (in this case, humans). This suggests that these functions play a particularly important role in mammalian evolution, the researchers said.

“From an evolutionary point of view, differences between species and individuals are very interesting,” Wagner said. “Comparing the two gives us an idea of ​​how much variation is tolerated within a species, and we can use this information to predict the ability to evolve.”

Finally, the researchers compared protein removal systems across species. There are two main systems responsible for clearing proteins in cells, and they found that one was similar across species, while the other was quite different across different mammals.

This protein turnover determines how quickly a cell can change state, Wagner added. “When a new signal comes in, the cell has to eject the proteins that were necessary for its previous state and make new ones,” he said.

And how quickly a cell changes state could be relevant to cancer.

“Healthy cells can be influenced by neighboring cancer cells,” says Wagner. “It will be important to understand whether protein turnover rates are related to how responsive cells are to tumor cell insults. Perhaps species that are more resistant to cancer, such as ungulates like cows and pigs, have cells that are less able to change states and are less susceptible to the signals from cancer cells.”

And understanding cancer susceptibility is just one possible application of this work, the researchers said. For example, they can begin to correlate protein differences with other traits that differ between species, Liu says.

Proteins undergo chemical modifications that occur when other molecules bind to a protein and turn it on or off. And these modifications contribute to traits that differ between and within species because they play important roles in influencing protein function. The researchers evaluated one type of modification in this study, phosphorylation, and found that variations in phosphorylation levels are largely unrelated to variations in protein abundance, providing another level of understanding of what drives biodiversity. Researchers will evaluate additional modifications in future work.

“It will provide a more complete picture,” Liu said, adding that biological differences between species and individuals shape biodiversity on Earth. “Measuring differences in both proteins and modified proteins between species will improve our understanding of biodiversity at the molecular level.”