Wednesday, September 2, 2015
Wanna know what's going on in poplar tree proteins?
If you spend a lot of time climbing trees, chances are you hate poplar trees. Wait. What I mean is: if you climbed a lot of trees as a child...because well-adjusted adults don't climb a lot of trees of course! chances are you hate poplar trees. They grow too fast and the branches aren't nearly as strong as their width might suggest.
However, some enterprising geneticists chose a poplar tree (the western balsa wood poplar (sounds strong, right?) rather than some more appropriate climbing tree as the first one to have its genome sequenced a few years back. This, of course, opens the poplar tree to proteomics!
In this new paper (ASAP at JPR) from Phil Loziuk et al., and linked to some guy named Muddiman, this team does a disturbingly thorough job of proteomic characterization of this tree. They first section the internal areas of the tree into whatever passes as tree organs and then use multistage fractionation and optimized FASP to end up with nearly 10,000 unique protein groups identified on a Q Exactive. The goal of the study was to hunt down transcription factors involved in cellulose production, which is never easy to do thanks to their low copy numbers. But when you get plant proteins down to the 10K unique level, you are going to be able to find just about anything, including transcription factors.
They pick the most interesting proteins by tree organ and develop an absolute quantification method that can be used routinely to assay the levels of the proteins most deeply involved in cellulose production.
I like this paper because its such a good story. "We set out to understand more about tree growth because its very useful for the lumber industry scientist...and here is a nice assay you can use." It really highlights how we can sit down with a scientist with a unique problem and apply our existing tools all the way to a solution.
Oh...and the sample prep/fractionation method is pretty interesting as well!