Saturday, May 9, 2015

Proteomics reveals the DNA repair process...and its more complex than we ever guessed!

(I HAD to use this image when I found it!)

Okay. so we've got a little over 3 billion base pairs of DNA in each of our cells (in the conventionally understood model). Every single time a cell divides we need to go through that 3 billion base pairs and make a complete and new and perfect copy.  And we've got to do this while still maintaining things like metabolism, respiration and rolling our eyes at reviewer suggested changes to the discussion sections of papers that make us want to just submit it somewhere else.

Sometimes mistakes are made (in the DNA, I mean).  And sometimes the process is messed up by things like UV radiation and exposure to oxidative radicals.  Even after the process is successfully completed, some of these things can come right into the cell and break the DNA strands clean in two.  If everything is working well a bunch of proteins come in and fix these mistakes and put the DNA back together.  If things aren't working well, then the break or mistake is allowed to stay there and that damage is duplicated when the cell divides again. This is how we get new mutations, but the goal is pretty much always to not get them.

We know LOTs about the DNA repair process.  Entire sections of big universities just study DNA repair mechanisms.  We have all sorts of cool proteins that we know are involved in this process.

So...why did M. Rasche et al., do all this proteomics work featured in this month's Science?  Cause it turns out that every other technique used over the years to identify proteins involved in DNA repair maybe just scratched the surface of the complexity of these mechanisms!

As their system, they messed up the DNA repair process of frog cells by stalling the replication forks. This is a common mechanism for this kind of study.  Essentially the DNA replication is just jammed up (normally by depleting the free nucleotide pool with something like hydroxyurea) that introduces DNA breaks.  The cool part is that you can jam the mechanism pretty much whenever you want.  Then they used their new technique they are calling Chromatin Mass Spectrometry, or CHROMASS...cause, you know, this field doesn't have enough acronyms... which essentially allowed them to quantify all the proteins that are coming to the rescue of the stalled fork breaks.

How'd it turn out?  Almost 100 proteins appear to be popping in to help out!  They identified all the known DNA repair proteins and scaffolding proteins that were expected.  And then have 50 or 60 new ones....and that's why its in Science!

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