Revealed: the mysterious ‘dark’ proteins that might play a big role in biology

‘Dark’ portions of the genome, which weren’t thought to hold instructions for making working proteins, have mostly been excluded from research. Now thousands of the proteins encoded by these genes have an official, new name — peptideins — that marks their inclusion in major gene and protein databases used by the life-sciences community. Dark proteins tend to be very short in amino acid length and lack evolutionary relatives in other organisms, which is part of the reason they have been omitted.

Ancient proteins rewrite rhino family tree

Proteins extracted from the remains of an extinct rhino species (Epiaceratherium itjilik) are among the most ancient ever sequenced. From a sample of enamel from the 23-million-year-old fossil, researchers were able to partially sequence 7 proteins. Integrating these proteins with genome data places Epiaceratherium in a new branch of the rhino family tree — one that split off between 41 million and 25 million years ago. The findings suggest that proteins survive better than researchers thought. This raises the possibility of gleaning molecular insights about evolutionary relationships, biological sex and diet from even older animals — maybe even dinosaurs.

Spatial proteomics

The average human cell contains roughly 10,000 different proteins, and to understand how cells function, you have to work out what those proteins interact with — and where. With advances in high-resolution imaging, mass spectrometry and machine-learning-assisted data analysis, spatial-proteomics researchers are mapping and tracking proteins with increasing detail at multiple scales, from subcellular compartments to tissues. The work is challenging and data-intensive, but findings have yielded insights into cellular biology and disease progression — not to mention, potential therapeutic strategies.

Homo antecessor finds its place in our family tree

The enigmatic hominin Homo antecessor has found its place in our family tree thanks to the 800,000-year-old proteins in fossil teeth. Researchers used mass spectrometry to analyse a sliver of enamel from a molar found in Spain’s Gran Dolina cave. The tooth reveals that H. antecessor was a close relative of the last common ancestor of humans, Neanderthals and Denisovans.