Evolutionary Proteomics Approach Opens View of How New Genetic Functions Appear


WEST LAFAYETTE, Ind. – The creation of genes with new functions is a major driver of developmental innovation in all living organisms. However, it is not clear how these genes acquire new functions over evolving time scales.

Duplications of entire genomes often occur, giving organisms redundant copies of genes that can mutate and acquire new functions. These duplicate genes are similar in sequence, and it is commonly believed that when species diverge, these genes retain the same functions for millions of years. This hypothesis leads scientists to believe that genes with similar sequences have the same functions, but that may not be true.

Purdue University Scientist Dan Szymanski and graduate student Youngwoo lee have developed a new high-throughput method to analyze these genes and the proteins they encode, identifying functional differences between a range of plant species, even among genes that appear to be the same. Their work suggests that these otherwise duplicated genes may give rise to new protein functions, as well as new interactions between protein complexes, which stimulate biological evolution and innovation in plants.

“Most analyzes of the evolution of plants are based on DNA and protein sequences, but our analysis is based on unique functional interactions or protein-protein interactions between related proteins. It goes way beyond the sequence and provides deeper functional clues, ”said Szymanski, professor at the Department of botany and phytopathology whose results were published in the journal Scientists progress. “We can develop hypotheses about how particular protein-protein interactions may have evolved during a changing environment or following a developmental change in the organism.”

Szymanski and Lee’s method consists in comparing the proteins and protein complexes of several plants by mass spectrometry. Using the model plant Arabidopsis thaliana along with cotton, soybeans and rice – all of which share a common ancestor – scientists have detected mass differences in evolutionary proteins. This suggests that these proteins, which would otherwise have to be the same in all different plants, have found ways to form new protein complexes and develop new functions. The same family of proteins could then be analyzed on a wide variety of species to test evolutionary patterns in protein-protein interaction data.

“As plants evolve and acquire duplications in their genomes, certain proteins mutate to develop a function not present in the ancestral gene. We can see this based on distinct masses of protein complexes, ”Szymanski said. “They bind to other proteins or to themselves, and sometimes these differences generate important new functions that are largely conserved in the lineage.”

While it can be argued that these protein-protein interactions formed by chance, Szymanski’s team provides evidence that these developments were driven by environmental circumstances and conserved in plants for millions of years.

Scientists give the example of carbonic anhydrase, a key protein for the transport of carbon dioxide. This protein would not have limited the productivity of plants in high carbon environments. Around 400 million years ago, however, levels of carbon dioxide in the Earth’s atmosphere were declining due to widespread colonization by plants. This new C02-The limiting environment may have made carbonic anhydrase more important, as its neofunctionalization into a more efficient form has been attributed to this interval in Earth history.

The process developed by Szymanski and Lee provides a molecular explanation of a common pathway towards protein neofunctionalization.

“This reveals which proteins have changed and how protein-protein interactions have evolved,” Szymanski said. “This can tell us a lot about the types of proteins that have innovated in response to changes in the environment or to plant development programs.”

The National Science Foundation’s Plant Genome Research Program funded Szymanski’s work.

Writer: Brian Wallheimer; 765-532-0233; [email protected]

Source: Dan Szymanski; 765-494-8092; [email protected]


ABSTRACT

Variants of multimerization as potential drivers of neofunctionalization 6

Youngwoo Lee and Daniel B. Szymanski

https://doi.org/10.1126/sciadv.abf0984

Duplications of the entire genome are common throughout evolution, creating genetic redundancy that can allow cellular innovations. New protein-protein interactions pave the way for diverse genetic functions, but at present, proteome-wide knowledge is limited on the extent to which variability in the formation of protein complexes results in neofunctionalization. Here, we used protein correlation profiling to test for apparent mass variability among thousands of orthologous proteins isolated from various species and cell types. Variants in the size of protein complexes were surprisingly common, appearing in some cases after relatively recent whole genome duplications or an allopolyploidy event. In other cases, variants such as those in the carbonic anhydrase ortholog group reflected the neofunctionalization of ancient paralogs that have been preserved in extant species. Our results demonstrate that the formation of homomers and heteromers has the potential to lead to neofunctionalization in various classes of enzymes, signaling and structural proteins.

Agricultural communications: 765-494-8415;

Maureen Manier, Head of Department, [email protected]

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