Indiana University biologists have found that specific types of RNA polymerase enzymes, the molecular machines that convert DNA into RNA, can differ in function based on variation in the parts -- in this case protein subunits -- used to assemble those machines.
The new findings on the synthesis and function of different RNA polymerases (Pols), including two RNA polymerases that lead author Craig Pikaard discovered over a decade ago -- the plant-specific enzymes Pol IV and Pol V -- indicate that subunit composition of the polymerases plays a role in selecting how some genes are silenced while others are not.
All eukaryotes -- a group that includes plants, animals, fungi and all other organisms with nuclei -- contain life-essential Pols I, II and III that are each built from different combinations of 12 to 17 protein subunits, with each of the three enzymes assigned specific, unique tasks in the cell. In 1999 while analyzing the newly sequenced genome of Arabidopsis thaliana, a member of the mustard family considered a model organism for experimentation in plant biology, Pikaard identified Pol IV and Pol V.
Pikaard's work has since shown that while the Pol IV and Pol V enzymes are not essential to life and are actually specialized forms of Pol II (the RNA polymerase responsible for generating RNAs that encode proteins), they play important roles in RNA-directed DNA methylation, a process that silences mobile genetic elements known as retrotransposons that can cause trouble if allowed to spread.
"In fact, most of the 12 protein subunits present in Pols II, IV and V are encoded by the same genes," Pikaard said. "Interestingly, among these common subunits are alternative forms of the ninth subunit, and the two forms of the ninth subunit (9a and 9b) are extremely similar, differing in only 8 of their 114 amino acids."
This high degree of similarity suggested 9a and 9b proteins might be redundant, but the Pikaard
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