Emergence of de novo protein coding genes from 'dark genomic matter' -- fact or fiction?

Proteins are the workhorses of the cell and, over billions of years, they have evolved an amazing plethora of extremely diverse and versatile structures with equally diverse functions.
Therefore, protein evolution echoes the evolution of all forms of life.
While it was previously assumed that all proteins result from old ones and that evolutionary emergence of new proteins and transitions between existing ones are rare or even impossible, recent advances in comparative genomics have repeatedly called some 10%-30% of all genes without any detectable similarity to existing proteins.
Even after careful scrutiny, some of those "orphan" genes contain protein coding reading frames with detectable transcription and translation but lack a homolog at the DNA level in outgroups.
Accordingly, some proteins seem to have emerged from previously non-coding 'dark genomic matter'.
Computational studies indicate that these 'de novo' proteins are disordered, fast evolving, weakly expressed and rapidly assuming novel and physiologically important functions.
They are therefore interesting to understand how genomic novelties come about, how structures evolve and might help fill important gaps in our understanding of how to construct novel functional proteins.
We investigated emergence of de novo proteins across insects and mammals, reconstructed their evolutionary history and predicted their structural properties.
Recently, we also expressed, purified and determined structural features of some of these novel proteins.
Our results indicate a pervasive origin of novel transcripts which are rarely posed to become protein coding genes but frequent rearrangements within and between protein coding genes, often along domain boundaries, which enable a swift creation and adaptation of novel proteins by reusing established parts and without the need to create novelties from scratch.

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