(C. elegans image borrowed from Genie Research)
This morning I learned that protein turnover slows down as most eukaryotic organisms age, which sounds like a dumb idea to me.
Fortunately, this great team in Belgium already knew about this and set up a really elegant C. elegans system to study this event and what is controlling it!
The method is really cool. They feed E.coli 15N or 14N containing NH4Cl. Then they put synchronized nematodes on plates of the labeled E.coli. They can have the worms eating labeled bacteria for however long they want and then move the worms to unlabeled bacteria. When they extract the proteins/peptides from the worms they can assess the protein turnover levels by comparing time vs heavy/light N. I don't know about you, but I'm impressed!
Not only can they assess overall protein turnover speed, but they can assess protein turnover speed of individual proteins. They pull a total of 54 samples and do 3 biological replicates for their downstream stats. The peptides were analyzed on an LTQ Orbitrap and peptide identifications were obtained with a pipeline that includes MS-GF+.
Even more cools stuff -- they have an R package that they developed that can do all the 15N/14N computations! You can get that here.
How'd they do?
The could accurately track turnover in nearly 900 peptides throughout all these samples that correspond to about 600 proteins. This gives them a really good picture of different cellular compartments and proteins of different molecular function.
In interpreting this data, the paper gets even better! Even in an organism this simple, turnover isn't just slowing down uniformly. It is a mixed bag. A few proteins even increase in turnover. They draw some really thought-provoking biological interpretations regarding the systems protecting eukaryotic cells from proteome collapse that is better to leave to this great open paper.
Clever system, great free software for the community, AND awesome biology? If you need an inspirational paper to start your week off right, I highly recommend this one!