Our lab investigates transcription by RNA polymerase III in the silkworm, Bombyx mori. Judging from their nucleotide sequences, we suspect that these two genes each contain a bend that may be crucial for transcription. If this is the case, we will want to know whether bending differences account for the different transcription properties of the two genes. I have worked with a post-doctoral fellow, Tom Steinberg, to determine whether there is a bend in the DNA in the upstream promoter in one or both of these genes and if so, to determine if bending differs between the two genes. The silkworm has developed a system to maximize the amount of silk it produces for spinning a cocoon.
Silk is a protein that has an unusual composition in that it consists of only a few amino acids.
One way that the silkworm maximizes silk production is to eliminate any limiting factors involved in alanine incorporation. One important, potentially limiting factor is tRNAala. The way that the silkworm boosts the supply of tRNAala is by having two classes of tRNAala genes activated in the silk gland, the site of silk manufacturing. These two genes have different transcriptional properties due to differences in their upstream promoter elements. There are other promoter elements, as well, that lie downstream, but these do not account for the observed transcriptional differences.