Transcription organization and mRNA levels of the genes for all 12 subunits of the fission yeast RNA polymerase II

Background: The RNA polymerase II (Pol II) of eukaryotes is composed of 12 subunits, of which five are shared among Pol I, Pol II and Pol III. At pres ent, however, little is known about the regulation of synthesis and assembl y of the 12 Pol II subunits. To obtain an insight into the regulation of sy nthesis of these 12 Pol II subunits, Rpb1 to Rpb12, in the fission yeast Sc hizosaccharomyces pombe, we analysed the transcriptional organization of th e rpb genes by use of the oligo capping method, and determined mRNA levels by quantitative competitive PCR assay. Results: The intracellular concentrations of the 12 Rpb subunits in growing S. pombe cells are different, within a range of 15-fold difference between the least abundant Rpb3 and the most abundant Rpb12. The transcription of one group of genes including rpb3, rpb4, rpb5, rpb6, rpb7 and rpb10 is main ly initiated at a single site, while that of the other group of genes for r pb1, rpb2, rpb8, rpb9, rpb11 and rpb12 is initiated at multiple sites. The promoters of the first group of genes contain the TATA box sequence between -26 and -62, while the second group of genes carry TATA-less promoters. Se veral common sequence segments, tentatively designated 'Rpb motifs', were i dentified in the promoter regions of the rpb genes. Competitive PCR analysi s indicated that mRNAs for Rpb1, Rpb3, Rpb7 and Rpb9 were among the group w hich had a low abundance, while the levels of Rpb6 and Rpb10 mRNAs were abo ut fivefold, and that of Rpb2 mRNA was about 40-fold higher than the Rpb3 m RNA level. Conclusion: The levels of rpb mRNAs do not correlate with those of Rpb prot eins. The protein-to-mRNA ratio or the translation efficiency is low for th e rpb1, rpb2, rpb3 and rpb11 genes, encoding the homologues of subunits bet a', beta, alpha and alpha, respectively, of the prokaryotic RNA polymerase core enzyme.