Yesterday I talked to Tom Silhavy about the periplasmic ATP-dependent DNA ligase that's co-induced with H. influenzae DNA-uptake genes (see old blog post here). He hadn't heard of this and was adamant that there is no ATP in the periplasm. So I did some more poking around.
I found papers about bacterial ATP-dependent ligases that function in 'non-homologous end joining' (NHEJ) reactions - these serve as last-resort repair mechanisms for double-strand DNA breaks that can't find a homologous template to use for repair. I emailed the author of a review, asking if the H. influenzae ligase belonged in this category. (He turned out to also be the person who had done the biochemical characterization of the H. influenzae ligase!)
He said that H. influenzae doesn't have the other NHEJ genes Ku and LigD, so it probably can't do NHEJ. I suspect the H. influenzae protein is in a different category of ligase, because a BLAST search with the H. influenzae ligase doesn't find known NHEJ ligases.
He also asked why I think it's targeted to the periplasm. At first I thought he meant, what do I think is the reason it's target to the periplasm, so I explained that I don't know. But then I realized he might be asking what is the reason I think it's targeted to the periplasm. I couldn't remember so I looked at it and its homologs using TIGR's HMM (hidden Markov model) location analysis function - this says that the H. influenzae protein and the four homologs I checked (Neisseria, Campylobacter, Shewanella and Thiomicrosomethingorother) all have a high probability of being periplasmic, with a single strong transmembrane domain close to the N-terminus. Tim VanWagoner, who also worked on the H. influenzae gene, also wrote that its Vibrio homolog is predicted to be periplasmic. Tom Silhavy had wondered if the apparent signal sequence might be an annotation error (wrong start site?), but this is very unlikely to be the case for all the homologs, so the odds are very high that these really are periplasmic.
I mentioned to Tom my idea that the ligase might be exported to the periplasm with an ATP already bound (the purified protein has its ATP covalently bound, ready for action). He said that, if that were the case, the protein would have to be exported by the Tat (twin argine translocation)system, because that's the only export system that can handle folded proteins. Luckily there's now a TatFind server, so I pasted in the various protein sequences, all of which had no recognizable TAT site in their first 35 aas.
How peculiar... We must be overlooking something important...
Bedazzled by alternate truth
4 hours ago in The Phytophactor