Different strategies for carboxyl-terminal domain (CTD) recognition by serine 5-specific CTD phosphatases

The phosphorylated carboxyl-terminal domain (CTD) of RNA polymerase II, consisting of ((1)YSPTSPS(7))(n) heptad repeats, encodes information about the state of the transcriptional apparatus that can be conveyed to factors that regulate mRNA synthesis and processing. Here we describe how the CTD code is read by two classes of protein phosphatases, plant CPLs and yeast Ssu72, that specifically dephosphorylate Ser(5) in vitro. The CPLs and Ssu72 recognize entirely different positional cues in the CTD primary structure. Whereas the CPLs rely on Tyr(1) and Pro(3) located on the upstream side of the Ser(5)-PO(4) target site, Ssu72 recognizes Thr(4) and Pro(6) flanking the target Ser(5)-PO(4) plus the downstream Tyr(1) residue of the adjacent heptad. We surmise that the reading of the CTD code does not obey uniform rules with respect to the location and phasing of specificity determinants. Thus, CTD code, like the CTD structure, is plastic.