New proteins ‘out of the blue’

Proteins are the most important component in all modern life forms. Hemoglobin, for example, transports the oxygen in our blood; photosynthesis proteins in the leaves of plants convert sunlight into energy; and fungal enzymes help us brew beer and bake bread. Researchers have long been exploring the question of how proteins mutate or arise over millennia. That completely new proteins – and with them new properties – could practically arise out of nothing was unthinkable for decades, in line with what the Greek philosopher Parmenides said: “Nothing can come from nothing” (ex nihilo nihil fit). In collaboration with colleagues from the US and Australia, researchers from the University of Münster (Germany) have now reconstructed how evolution shapes the structure and function of a newly emerged protein in flies. This protein is essential for male fertility. The results have been published in the journal Nature Communications

Until now, it has been believed that new proteins arise from pre-existing proteins – through a duplication of the underlying genes and through a series of small mutations in one or both gene copies. Over the past decade, however, a new understanding of protein evolution has emerged: proteins can also develop from so-called non-coding DNA (deoxyribonucleic acid) – in other words, from that part of the genetic material that does not normally produce proteins – and can subsequently develop into functional cell components. This is surprising for several reasons: for years it was believed that to be functional, proteins had to take on a highly developed geometric shape (a 3D structure). It was further believed that such a form could not evolve from a gene that emerged randomly, but that a complex combination of amino acids would be required for this protein to exist in its functional form.

Despite decades of trying, researchers worldwide have failed to construct proteins with the desired 3D structures and functions, leaving the “code” for the formation of a functioning protein essentially unknown. While this task remains a puzzle for scientists, nature has proven to be more adept at the formation of new proteins. A team of researchers led by Prof. Erich Bornberg-Bauer, of the Institute for Evolution and Biodiversity at the University of Münster, found, by comparing the newly analyzed genomes in numerous organisms, that species differ not only by duplicated protein-coding genes that have been adjusted in the course of evolution. In addition, proteins are constantly (re) formed de novo – that is, without any related precursor protein going through a selection process.

The vast majority of these de novo proteins are useless, if not somewhat harmful, as they can interfere with existing proteins in the cell. Such new proteins are quickly lost after several generations, because organisms carrying the new gene that codes for the protein have impaired survival or reproduction. However, a select number of de novo proteins appear to have beneficial functions. These proteins integrate into the molecular components of cells and eventually become indispensable after millions of years of small adjustments. There are some important questions that many researchers ask themselves in this context: What do such new proteins look like at birth? How do they change and what positions do they assume as ‘new kids on the block’? Led by Prof. Bornberg-Bauer’s group in Münster, an international team of researchers has answered this question in detail for Goddard, a fruit fly protein essential for male fertility.

The research took place on three related fronts, spanning three continents. At the College of the Holy Cross in Massachusetts, USA, Dr. Prajal Patel and Prof. Geoff Findlay CRISPR / Cas9 genome editing to show that male flies that do not produce Goddard are sterile, but otherwise healthy. Meanwhile, Dr. Andreas Lange and Ph.D. student Brennen Heames from Prof. Bornberg-Bauer’s group used biochemical techniques to predict the shape of the new protein in modern flies. They then used evolutionary methods to reconstruct Goddard’s likely structure ~ 50 million years ago, when the protein first emerged. What they discovered was quite a surprise: “The ancestral Goddard protein was already very similar to those found in fly species today,” explains Erich Bornberg-Bauer. “From the outset, Goddard contained some structural elements called alpha helices, which are believed to be essential to most proteins.” To confirm these findings, the scene shifted to the Australian National University in Canberra, where Dr. Adam Damry and Prof. Colin Jackson used intensive computer simulations to verify the predicted shape of the Goddard protein. They validated Dr. Lange and showed that despite his young age, Goddard is already quite stable – although not as stable as most fly proteins that are believed to have been around for longer, perhaps hundreds of millions of years. .

The results are consistent with several other current studies, which have shown that the genomic elements that make up protein-coding genes are often activated – tens of thousands of times in each individual. These fragments are then sorted through the process of evolutionary selection. Those that are useless or harmful – the vast majority – are quickly discarded. But those that are neutral, or are somewhat beneficial, can be optimized over millions of years and turned into something useful.