Field of Science

progress (?) on the ligase puzzle

The NHEJ expert said that he thought the periplasmic assignment of the H. influenzae ATP DNA ligase must be an error.  I was discussion the ligases with a colleague who works on Campylobacter (which also has one of these ligases) and she suggested I try running the sequences through the program PSORT-b, which is particularly good with bacterial proteins.  

PSRT-b could not assign a high-probability location to most of the ligases I tried, suggesting that the HMM method used by TIGR's database may be overconfident.  I was also surprised to find that its BLAST search pulled up some NAD-dependent ligases as matches to the ATP-dependent ligase sequences I tried.  I had been thinking that the two families had very dissimilar sequences, but maybe I'm wrong in that. 

The possibility that these ATP-dependent ligases act in the cytoplasm is interesting, as the competence-induction of the H. influenzae one may mean that it contributes to the postulated replication-arrest problem rather than to DNA uptake.

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