Decoding the informational properties of the RNA polymerase II Carboxy Terminal Domain

On the computational ability of the RNA polymerase II carboxy terminal domain

The RNA polymerase II carboxy terminal domain has long been known to play an important role in the control of eukaryotic transcription. This role is mediated, at least in part, through complex post-translational modifications that take place on specific residues within the heptad repeats of the domain. In this addendum, a speculative, but formal mathematical conceptualization of this biological phenomenon (in the form of a semi-Thue string rewriting system) is presented. Since the semi-Thue formalism is known to be Turing complete, this raises the possibility that the CTD – in association with the regulatory pathways controlling its post-translational modification – functions as a biological incarnation of a universal computing machine.

The Ess1 prolyl isomerase: traffic cop of the RNA polymerase II transcription cycle

Ess1 is a prolyl isomerase that regulates the structure and function of eukaryotic RNA polymerase II. Ess1 works by catalyzing the cis/trans conversion of pSer5-Pro6 bonds, and to a lesser extent pSer2-Pro3 bonds, within the carboxy-terminal domain (CTD) of Rpb1, the largest subunit of RNA pol II. Ess1 is conserved in organisms ranging from yeast to humans. In budding yeast, Ess1 is essential for growth and is required for efficient transcription initiation and termination, RNA processing, and suppression of cryptic transcription. In mammals, Ess1 (called Pin1) functions in a variety of pathways, including transcription, but it is not essential. Recent work has shown that Ess1 coordinates the binding and release of CTD-binding proteins that function as co-factors in the RNA pol II complex. In this way, Ess1 plays an integral role in writing (and reading) the so-called CTD code to promote production of mature RNA pol II transcripts including non-coding RNAs and mRNAs.

Synthetically engineered rpb1 alleles altering RNA polymerase II carboxy terminal domain phosphorylation induce discrete morphogenetic defects in Schizosaccharomyces pombe

In this report the phenotypic effects of systematic site-directed mutations in the fission yeast RNA pol II carboxy terminal domain (CTD) are investigated. Remarkably, we find that alterations in CTD structure and/or phosphorylation result in distinct phenotypic changes related to morphogenetic control. A hypothesis based upon the concepts of “informational entropy” and “algorithmic transformation” is developed to explicate/rationalize these results.