You can flash SuperSU from recovery ([CWM][1] or [TWRP][2]). I ran into something similar yesterday while applying the OTA to a rooted Nexus 5, and this fixed it. 


  [1]: http://download.chainfire.eu/204/SuperSU/CWM-SuperSU-v0.94.zip
  [2]: http://download.chainfire.eu/365/SuperSU