Diaminopurine in cyanophage S-2L DNA

Sunday, 8 November 2015

Diaminopurine in cyanophage S-2L DNA


There is a Nature paper from 1977 reporting a cyanobacterial phage, S-2L, that uses diaminopurine in its DNA instead of adenine. diaminopurine has two amine groups as opposed to one, so can bind more tightly to thymine, thus changing the behaviour of its DNA and tricking its host.


The strange thing is that this cool discovery went nowhere even though it would have some really interesting applications. In fact, this paper was followed by two others, then a hiatus and then two papers in the 90s about melting temperature. No cloning, no nothing.
The phage was lost as there is a patent that gives its sequence. The sequence is unhelpfully unannounced, but the patent among the really boring bits has claim 270, which says:
On the other hand, it seems very likely that the D-base is formed by semi-replicative modification. Between the two biosynthesis routes of dDTP formation described above, the identification of a succinyladenylate synthetase gene homologue called ddbA (deoxyribodiaminopurine biosynthetic gene A) leads to the conclusion that it is the second route which is probably taken during phage infection (FIG. 2).
Several tests have been carried out in order to determine the activity of the corresponding protein. The results suggest that the expression of ddbA allows restoration of the growth of a strain of E. coli expressing the yaaG gene of Bacillus subtilis [yaaG (now dgk) encodes  deoxyguanosine kinase] in the presence of a high concentration of dG (10 mM). On the other hand, 2,6-diaminopurine becomes toxic (10 mM) to E. coli when it is in phosphorylated form (which has been tested in the same strain of E. coli expressing the yaaG gene of Bacillus subtilis i.e. MG1655 pSU yaaG) which makes it possible to have a screen in order to identify in vivo the complete biosynthesis route of the D-base.
So they have a purA homologue, but not a purB homologue or a kinase. This means that either Synechococcus purB and adk promiscously do the reactions, which seems odd given that the phage would give them a negative selection, or that an analogue eluded them. Parenthetically, the people that filed the patent were not the people who found the virus and no paper was published about it even though the first author of the patent studies odd nucleobases.
One interesting thing from the genome is the presence of many polymerases and of DNA gyrase, which is due to the odd DNA.
In conclusion, it is a real shame research into this curious pathway was minimal and has not progressed as it would be a perfect toolkit for synthetic biology.

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