Wang et al. (Cell research 2014) and Tsai et al. (Cell 2014) recently describe a substantially improved cryo-EM of the Mediator Complex which permitted an unambiguous and topsy-turvy assignment of the Head, Middle and Tail modules.
Mediator is a gigantic evolutionarily conserved multi-protein complex comprising over 25 different subunits (~ 1.2 MDa) that plays major roles in both basal and activated transcription (Malik and Roeder, 2010; Poss et al., 2013; Yin and Wang, 2014). Its sheer size, low abundance and conformational variability have prevented the high-resolution structural determination of the entire complex and thus the exact Mediator architecture is still a matter of debate (Larivière et al., 2012). To date, high-resolution structures of the 7-subunit Mediator head module (Imasaki et al., 2011; Larivière et al., 2012; Robinson et al., 2012) and several single subunits or domains are available (Baumli et al., 2005; Bontems et al., 2011; Hoeppner et al., 2005; Larivière et al., 2006; Larivière et al., 2008; Milbradt et al., 2011; Schneider et al., 2011; Thakur et al., 2009; Vojnic et al., 2011; Yang et al., 2006).
In addition, structural information of full Mediator at low resolution have come from cryo-EM studies (Asturias et al., 1999; Bernecky et al., 2011; Bernecky and Taatjes, 2012; Cai et al., 2009; Davis et al., 2002; Elmlund et al., 2006; Knuesel et al., 2009; Näär et al., 2002; Taatjes et al., 2002; Taatjes et al., 2004; Tsai et al., 2013; Wang et al., 2013).
A major point of agreement that emerges from these extensive biochemical studies is that Mediator subunits are organized into three core modules (Head, Middle, Tail) and a dissociable CDK8 kinase module. However, information about subunit localization and boundaries of the three core modules has remained rather elusive, even contradictory. For example a recent cryo-EM of yeast Mediator at 28 Å resolution identified a previously additional independent module referred to as the arm domain (Cai et al., 2009).
In two recent reports, the Cai (Wang et al., 2014) and Asturias (Tsai et al., 2014) labs describe a cryo-EM analysis that completely redefine the modular organization of the core Mediator. In particular the head module was previously assigned to one end of the Mediator structure with the middle and tail modules folded back on one another to from the upper portion of Mediator (Chadick and Asturias, 2005).
Using either tagged or deleted individual subunits combined with unequivocal docking of the X-ray structure of the Head module, the authors arrive at an impressive improved cryo-EM reconstruction of Mediator at a resolution of ~ 18 Å. And in a dramatic topsy-turvy twist, the Head and Middle modules form now the upper portion while the dense domain at the base corresponds to the Tail. As a consequence of the enhanced resolution, previously unassigned metazoan-specific subunits are now clearly localized. For example, MED27, MED28, MED29 and MED30 make extensive contacts with the Head module while MED26 associates with the Middle module.
Does this completely new pattern of modules rearrangement provide a more concrete view of the conformational changes that these modules undergo upon interaction with the RNA polymerase II ? Previously, the most prominent change resulted from the relative rotation and translation of the Middle and Tail modules that leads to a complete repositioning of the Middle module (Cai et al., 2009). These module movements triggered by formation of the holoenzyme are still carried on but from now on that is the Head and the Middle modules that undergo a coordinated rotation.
These observations directly challenge the previous holoenzyme model in which the reported RNA pol II binding site was located near the Head module. Astonishingly, the entire interaction surface of the Head module is now highly exposed and extensive Mediator/RNA pol II contacts are mediated through the Middle and Tail modules.
In the future, with the cryo-EM resolution revolution (Kühlbrandt 2014), the near-atomic resolution of full Mediator and even of the full transcription pre-initiation complex (PIC) may soon become a reality.