An Explosion of Hidden Messages

Looking for hidden messages in multiple genomes

We should not jump to the conclusion that ATGATCAAG/CTTGATCAT is a hidden message for all bacterial genomes without first checking whether it even appears in known ori regions from other bacteria. After all, maybe the clumping effect of ATGATCAAG/CTTGATCAT in the ori region of Vibrio cholerae is simply a statistical fluke that has nothing to do with replication. Or maybe different bacteria have different DnaA boxes.

Let’s check the proposed ori region of Thermotoga petrophila, a bacterium that thrives in extremely hot environments; its name derives from its discovery in the water beneath oil reservoirs, where temperatures can exceed 80º Celsius.

This region doesn’t contain a single occurrence of ATGATCAAG or CTTGATCAT! Thus, different bacteria may use different DnaA boxes as “hidden messages” to the DnaA protein.

Significance of the Frequent Words Problem

Application of the Frequent Words Problem to the ori region above reveals that the following six 9-mers appear in this region three or more times:

AACCTACCA	AAACCTACC	ACCTACCA

CCTACCACC	GGTAGGTTT	TGGTAGGTT

Something ...