mRNA degradation and RNA processing in the yeast S. cerevisiae
Mechanism and Control of mRNA Turnover –
Eukaryotic cells require several layers of regulation for gene expression. For cells to have a rapid response to environmental conditions, an important mechanism is translational control, which can quickly alter the proteins produced by the cell. Key to this regulation could be evolutionarily conserved cytoplasmic RNA granules called P-bodies which consist of non-translating mRNA, translational repressors, and mRNA decay factors (depicted in Figure 1). They are sites of mRNA decay as well as translational repression. Their role in the eukaryotic mRNA life cycle is diagramed in Figure 2. Since these granules contain proteins that are essential for decay and translational repression, they may act as control centers that determine the fate of the mRNA: should it be translated, degraded or moved into long-term storage?
Figure 1. P-bodies in yeast. A component of the P-bodies, the mRNA decapping enzyme, is GFP tagged. In exponential growth (left panel), P-bodies are largely absent. During starvation conditions (right panel), translation is inhibited and the protein and mRNA together form P-bodies with the assistance of Pat1. (From Nissan and Parker, 2008).
Decay of mRNA represents an irreversible alternative to translational control. In general, mRNA decay begins by shortening of the poly(A) tail of mRNA by cytoplasmic deadenylases. After deadenylation, one major pathway of mRNA decay leads to the removal of the 5’ 7-methylguanosine (m7G) cap of the mRNA. Decapping effectively ends the life of the mRNA by rapid 5’-3’ degradation. In addition to the decapping enzyme, several protein serve to accelerate the rate of decapping in vivo.
Figure 2. The Eukaryotic mRNA cycle. Messenger RNAs are transcribed, processed and exported from the nucleus and enter active translation. However, with the assistance of the Pat1 protein, they can leave translation and form RNA granules called P-bodies. There the fate of the mRNAs can be determined: should they be destroyed or instead re-enter translation?
Both decay and translation are linked, for example the decapping rate is in competition with the translation initiation rate. To understand these processes and their linkage, it will be important to determine the biochemical functions of key proteins that repress translation and promote mRNA degradation.
A key protein with roles in both systems is Pat1. It accelerates the rate of decapping in vivo, and demonstrates the strongest effect on decapping of any protein except for members of the decapping enzyme. It also exhibits one of the strongest effects on the formation of P-body RNA granules. Pat1 also plays a central role in mediating translational repression. Furthermore, Pat1 is conserved in eukaryotes, and orthologs are found in P-body like RNA granules in S. cerevisiae, Drosophila, C. elegans, and mammalian cells. Finally, Pat1 knockdown in Drosophila S2 cells affects the degradation of certain miRNA targets.
Role of RNA Granules in Biology
An important issue in eukaryotic cells is the biogenesis and function of RNA molecules. RNA is the essential bridging molecule between the genetic code and protein, and is perhaps even the origin of life. We study how cells produce or regulate these processes leading to effects on the expression of genetic information. Our research concentrates on the involvement of RNA in control of gene expression.
Eukaryotic cells require several layers of regulation for gene expression. For cells to have a rapid response to environmental conditions, an important mechanism is translational control to quickly alter the proteins being produced by the cell. Key to this regulation could be evolutionarily conserved cytoplasmic RNA granules called P-bodies, which consist of non-translating mRNA, translational repressors, and mRNA decay factors.