Transition studies 

 in plants             by Rolf Baumberger 

The Pushmi-Pullyu-Code 

 There will be an update shortly

Posterity will admire you, it will avenge you, my father

The importance of short tandem repeats  as (TATATATATATA) could be far greater than generally believed. These noncoding STRs in the introns may play a significant role in regulating plants' master and other factors. They act as software and hardware at the same time. Moreover, they are quick to alter their functional length in a flash. - Please note that such STRs appear very quickly but also disappear. In very stable organisms they are harder to find.

The Pushmi-Pullyu-Code


Especially long TATA-repeats can build in mRNA double stranded portions

that act as a signal for spliceosome etc. 


We estimate that the length of the strings code for gene-activity.

Especially when there are more than 11 pairs long.
STRs in introns (short  tandem repeats in introns of regulating factors)
A):
AA{TATATATATATATATATATATATATATATATATATATA}CC  | high activity |
 AA{TATATATATATA}CC  | low activity |

We saw that more than 15% of the Diplacus regulator genes in the genome have such specific inclusions. The lengths of these strings are variable. Their lengths may alter even during the lifespan of a plant individual. Such «editing alterations.» have a functional value.


 

R2R3MYB2 of Diplacus puniceus, the main anthocyanin driver in red floral petals, has TATATA sequences right after the second exon. When long, in the case of the red ecotype, the long hairpins may influence the spliceosomes. Short hairpins do not act as an activator of the spliceosome, as in the yellow ecotype. Interestingly, orange flowered T-plants have such hairpins in between lengths. For the first time, we can hypothesize about the coloration of the floral petals in a genotype-to-phenotype way. Also, around the promoter of this factor, we found long TATA motifs in red puniceus and short motifs in yellow ecotypes. Although the mechanism by which these hairpins alter is still unclear, it is a significant step toward unraveling the process of evolution in this case.

 

 

 

One cannot go further: Intron section of LIF2, the Diplacus plant innate immune response protein. Database: All available genomes from red and yellow flowered Diplacus individuals. Red flowered strings tend to the reading TTTTTTTAAAAA. The yellow ecotype individuals tend to be a mixture of T and As. The result is a long hairpin for the red kind and a shorter pin for the yellow kind. Generally, long hairpins force the gene to be more active. One can see a quantum decision for this problem. It is a rather dynamic state and a kind of molecular thinking. 

 

We have to get used to evolution (in this case, speciation), which can be a self-regulating process. - We take on the role of the observer. The more mistakes we make in our observations, the more precise our picture of what is happening needs to be.

Here is the intron representation of E1 of the 10-megadalton dehydrogenase complex. The oscillation between the red ecotype and the yellow one is visible (T<->C). The matter is intertwined: a regulatory change of a master factor (here R2R3MYB2) also leads to regulatory changes in other factors (E1).

see: https://doi.org/10.1016/j.jmb.2022.167920


Interestingly, the intron STR of the endoplasmatic membrane protein C16 shows four different sequencing, resulting in different hairpin lengths in four taxa. The four inspected taxa were very closely related.

  

Isn't it an intelligent way to constitute a hairpin?

Tool: http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi