Advanced mass spectrometry uncovers a tiny protein with important implications
Joanna Cummings |
Meet NoBody (non-annotated P-body dissociating polypeptide): a new, functional human microprotein, discovered and characterized by biochemists using cutting-edge gene sequencing and proteomics technologies at Yale University (1).
The team examined myeloid leukemia cells, first removing larger proteins, then using liquid chromatography-mass spectrometry (LC-MS) based proteomics to uncover the amino acid sequence of each of the more than 400 microproteins that remained. Having discovered a veritable treasure trove of previously unknown proteins, the researchers set out to find out their function (if any) in the body.
“Evolutionary sequence conservation is a great way to help you find function because if the protein sequence of a gene doesn’t change, that probably means it is doing something important and changes to the sequence would be detrimental,” explains co-senior author Alan Saghatelian. “Sarah Slavoff (co-senior author) decided to dig into the function of the gene for these microproteins, and through functional proteomics, linked NoBody to proteins that had been characterized in mRNA decay.” In other words, NoBody helps to recycle genetic material in the cell.
Recent advances in gene sequencing have enabled detection of the small open reading frames (smORFs) that encode microproteins like NoBody, Saghatelian says. “Without RNA-Sequencing we could only have found about a third of smORFs. In addition, mass spectrometers have gotten so much more sensitive that it really allows us to dig a lot deeper into the proteome to find them. Ten years ago, the same experiment might have yielded 10–20 percent of what we are seeing today.”
Saghatelian says that the discovery of NoBody has major implications: “First, it points to the fact that digging into the biology of microproteins is going to lead to new biological insights, and in some cases we will learn something about a disease, which we can use to develop new treatments.” Second, he says, it has contributed to understanding the regulation of mRNA decay. “mRNA levels are used to do so much in biology, but most of this is considered from a production viewpoint (which is to say, transcription). However, degradation of particular mRNAs will be important too. The field has tons of room to grow – there is still a lot we don’t understand.”
The lab is now focused on finding and characterizing more microproteins, as well as building better technology to identify the most interesting ones to study. “In terms of biology and the relation to disease, my feeling is that we’re only at the beginning,” concludes Saghatelian.
- NG D’Lima, “A human microprotein that interacts with the mRNA decapping complex”, Nat Chem Biol, 13, 174-180 (2016)