Due date for project write-ups: Dec. 11
First of all, the yeast genome has about 6,400 genes. The genes are of course transcribed into mRNA (and processed by the addition of a 5' cap and a 3' polyAAA tail) and those mRNA are of course translated into proteins. When the mRNA are through being translated, they need to be degraded. Normally, this happens by the mRNA being somehow recognized by the translation machinery and targeted for degradation. First, the PolyAAA tail is removed and then the cap is removed by DCP1. Then the mRNA is degraded 5' to 3' extremely quickly by XRN1, which is an exoribonuclease. However, there is an alternate decay pathway that focuses on abbarent mRNA. These mRNA are ``born'' with a premature stop codon upstream of the normal stop codon. These errors (premature stop codons) can result from errors in the DNA, errors in transcription or errors in splicing. This pathway that recognizes these mRNA and degrades them is called ``nonsense-mediated mRNA decay'' (NMD). There are 3 proteins in this pathway that work together to recognize error-containing mRNA and degrade them using the usual proteins (XRN1 and DCP1). These proteins are known as UPF1, UPF2 and UPF3. If any one of these is removed, the pathway doesn't work and anything that it was supposed to degrade just builds up in the cytoplasm of the cell. Recently, there has been a discovery made by Lelivelt, et al., 1998 (http://126.96.36.199/default.htm) that there are also normal/wildtype mRNA that are degraded by this pathway also. Since we, as a field, previously thought that NMD was a pathway dedicated to getting errors out of the cell, this came as a considerable shock. Lelivelt discovered using an AFFY metrix screen, that approximately 350 of the 6,400 yeast mRNA are degraded by this pathway. One of the normal/wildtype mRNAs that is degraded by this pathway is called PPR1. PPR1 is a transcriptional activator that regulates many of the URA genes (Uracil biosynthetic pathway) in yeast. Since PPR1 regulates many genes, if NMD ceases to function, anything that PPR1 regulates will also build up in the cell. These types of mRNA's are called ``indirect'' targets. Thus, some mRNA are actively sought out by the pathway to be degraded and others are only effected because their regulators are targets of NMD.