This image of human kidney cells shows NoBody (green), P-body markers (red), cell nuclei (blue), and NoBody interacting with P-bodies (yellow).
Image credit: MIT/Yale University
Researchers from Yale University in New Haven, CT, and the Salk Institute in La Jolla, CA, describe how they found their new microprotein – which they name NoBody (non-annotated P-body dissociating polypeptide) – along with hundreds of others, in the journal Nature Chemical Biology.
Co-senior author Sarah Slavoff – assistant professor of Chemistry and Molecular Biophysics and Biochemistry at Yale – says their findings suggest that microproteins such as NoBody appear to play a role in many biological processes, as well as disease. For instance, many neurological diseases feature groupings of proteins.
Proteins are the workhorses of the cell. Their genetic blueprints are encoded in DNA and obediently carried to the cell’s protein-making machinery by molecules called messenger RNA – dubbed mRNA.
Since the completion of the Human Genome Project in 2003 – where scientists sequenced and mapped all of the genes for building Homo sapiens – we have learned a lot about proteins, their associated genes, and the RNA mechanisms that translate them.
Traditional sequencing leaves blind spots in the genome
An important control mechanism for cell health is to avoid making too much of a protein. Scientists have discovered that one way this is regulated is by timely recycling of the mRNA; it stops protein synthesis.
The new study shows that the previously unknown protein NoBody plays a key role in mRNA recycling.
Sophisticated tools have emerged to refine and speed up sequencing and mapping of human genes, even to the point of being able to scan the whole genome of IVF embryos for disease mutations.
However, the pattern-seeking software that the now traditional genomic tools rely on are not always reliable enough to find what might be hiding in plain sight – such as tiny proteins with important jobs. Prof. Alan Saghatelian, Salk professor and one of the senior authors of the new paper, explains:
“Despite how much we know about the human genome, there are still blind spots in the genome discovery algorithms. You can sequence the whole human genome and never know a protein, like this one, was there because it’s too short and falls below the usual length requirement for gene assignment algorithms.”
Researchers developed new microprotein detection strategy
By combining genomic sequencing and liquid chromatography-mass spectroscopy proteomics, the researchers developed a new microprotein detection strategy to look for tiny proteins that conventional genome sequencing would overlook.
They took the contents of cells from a commonly studied myeloid leukemia cell line and removed the larger proteins. Using the new strategy, they determined the amino acid sequences of every protein that was left.
To find out which genes coded for these proteins, the team developed a computational method to make a database containing every possible microprotein from all of a myeloid cell’s mRNAs – which they sequenced using genomics techniques.
The researchers then used the custom database to search their new protein sequences for matches to real proteins and found over 400 new microproteins, including NoBody.
When they studied NoBody more closely, the researchers found that it interacts with proteins that help regulate the recycling of mRNAs at points inside cells known as P-body granules. Clusters of mRNA and proteins that perform the first step in breaking down the mRNAs accumulate at these points.
They suggest that changes to NoBody levels inside cells could disrupt RNA recycling, which is an important cell-clearing process. The discovery could lead to new treatments that target RNA dysfunction.
“The discovery of NoBody and its function in mRNA recycling suggests that at least some of the hundreds of other microproteins that we have found might also be functional, which is an exciting proposition,” says Prof. Saghatelian.
“The broadest significance of this work is that even in a well-studied biological process, a microprotein has been right there under our noses, undetected, all this time.”
Prof. Sarah Slavoff