I have been studying an expression of a gene that I called DET1, which involved in cyanide detoxification. This gene has a transposable element (TE) inserted into the gene. As a result, its transcript was truncated.
I removed the TE from the gene (DET1_NoTE) and overexpressing it in arabidopsis. For a control, I found an orthologous gene from arabidopsis, AtDET1. As expected, overexpression of DET1_NoTE was comparable to AtDET1 as shown in a cyanide detoxification assay.
However, when DET1_NoTE and AtDET1 were expressed under either DET1 promoter or AtDET1 promoter, the AtDET1 plants appeared to have a significantly stronger cyanide detoxification ability when compared to DET1_NoTE plants.
This makes me wonder if, after the TE insertion that alters the transcriptional start site of DET1, mutations could have been accumulated in the regions that no longer got transcribed and hence breaking down the relationship between the gene and its promoter, and this could be viewed from DET1 promoter and DET1 is no longer working efficiently.
Is there any similar observation that you might know of?
From my point of view, it's too speculative to make this assumption, unless you have more concrete evidence. Because when you see AtDET1 displays higher activity than DET1, it only tells you that AtDET1 protein has a higher catalytic efficiency due to its amino acid differences from DET1.
TE insertion causing transcriptional downregulation is quite common, especially in some cereal crop genomes. To verify your assumption, you can search the pangenome data if any available. If this TE insertion occurs recently, there should be some varieties without the TE. Comparing their promoter sequence and coding region variations may give you some clues.
- Badges
- Science topic
- Similar topics
- Agriculture
- Horticulture
- Seeds