Proteomics and metabolomics of B. subtilis cells and spores!

 

Honestly, I figured that given how good the maps of the pathways of how things worked in B. subtilis were when I was in grad school -- largely due to decades of work in Peter Setlow's lab - that we had this bacteria all figured out by now.... 

But, of course we don't, right? When Dr. KBJ was on our podcast she dropped the perceptive bomb on us that we don't even have functional annotation for 1/2 of the genes in E.coli, and that has to be the most studied of the bacteria!  So, time for some Metabolomics and Proteomics of B. subtilis.... from ... Peter Setlow....?....

I had to check Scholar to make sure I wasn't off by a score of years and - yes -  I found a Peter Setlow paper from 1964. And 13 papers in 2023! What a career he is having! 

The paper walks you through a couple of different extraction methods in order to find something universally applicable to a tough bacterium and to extremely ridiculously tough bacterial spores. There is an undertone of concern that by using different required extraction methods for two of the life cycle stages of this organism that is actually what you're seeing rather than true effects, which makes sense. I do think that this is one of the first papers I've seen where the metabolomics and proteomics were both done on a TIMSTOF. I've yet to take the metabolomics plunge with the TIMS and it is nice to see it working so well. It is also explained well. So if you're interested in trying it, this is as nice of a tutorial as I've seen, particularly on the data processing side. 

They use Bruker's solution for the metabolomics and MaxQuant for the proteomics and all the files are up on MASSIVE. It appears to be a very solid study. I do have a minor qualm about the implication in the abstract graphic that extensive correlative analysis was performed between metabolites and proteins. If that was done, I don't see evidence of it here. There is a functional analysis of a single pathway that made the main paper, but I'd probably save a full functional analysis of these data for second paper as well. Now -- the really cool thing, of course - would be to apply this same method across the sporulation cycle -- and then to do the correlative analysis, and with an extraction method that works on both ends of the cycle, I won't be surprised to find out that was the plan all along. Probably ought to set an scholar alert for it.