|Transcription from DNA|
The enzyme found in E.coli that produces mRNA (and rRNA and tRNA) is simply called RNA Polymerase. In general, one polymerase transcribes all RNA classes in bacteria. In higher organisms, we have an RNA polymerase for each class of RNA: RNA Pol I (rRNA), PolII (mRNA) and PolIII (tRNA). one of the most interesting polymerases is Reverse Transcriptase, which takes RNA templates and converts them to DNA (I will be covering RT as a separate molecule of the month in the future, in view of its special role in AIDS infections).
|Eukaryotic RNA Polymerases|
comprise multiple subunits
A simple RNA Polymerase will catalyse the polymerisation of RNA, but one of the most interesting features of these molecules (apart from their catalytic mechanism and their level of fidelity), is that they are capable of being regulated in a range of different ways. Organisms from all walks of life are able to activate or repress their RNA Polymerases; or put differently, all organisms can regulate transcription. This may be achieved in one of two generic ways. Firstly, proteins can interact with the core polymerase machinery to change its shape, and as a consequence the catalytic site is either shut down or, in contrast activated. This phenomenon is classically referred to as allostery (from the French for "other site"). In Biology, when an enzyme is modulated in function by the binding of a small molecule, or macromolecule, to a site that is remote from the active site; this is generally a strong indication of regulation. The toggling of enzyme activity in situ, is one of the key mechanisms underpinning the development of complexity in higher organisms (it is also a major "economy saving" device used by cells to control the flux of metabolic intermediates in intermediary metabolism). Allostery goes hand in hand with the second way that RNA Polymerases can be regulated: a phenomenon known as post-translational modification, a topic we shall discuss at a later stage in some detail. However in simple terms, the addition of low molecular weight adduct to a target protein (usually through enzyme-mediated transfer) such as a phosphate or a methyl group, can also induce a shape (conformational) change in the protein, which can indirectly activate or inhibit as with allostery (see the cooperative binding curve for Haemoglobin in an earlier Blog).
Comparisons between the RNA Polymerases in bacteria and animals
The three eukaryotic RNA polymerases
"On the nature of allosteric transitions: a plausible model": A landmark paper from 1965, in the field of allostery: a substantial paper with a secondary focus on molecular symmetry in proteins. A "must read" for all biochemist. Jacques Monod, Jeffries Wyman and Jean-Pierre Changeux all made major contributions in Science in its widest definition between 1930 and 1990!
Mark Ptashne: another pioneer in the molecular biology of transcription: from repressors in bacteria to transcription factors in yeast: a remarkable career punctuated by some of the most elegant experiments (he's the accomplished violinist on the left!).Roger Kornberg's lab (awarded the Nobel Prize for determining the structure of RNA Polymerase from yeast): a truly remarkable piece of Biochemistry and X-ray crystallograohy. Robert Tjian: a pioneer in the biochemistry of eukaryotic transcription: I first came across his work in the early '80s along with that of Robert Roeder.