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cluster K terminases

| posted 15 Jul, 2019 09:46
Hi All,
I am QCing a cluster K4 phage (Malthus) and am trying to make decisions about calling small and large subunit terminases vs calling a single terminase gene. The authors have called a small subunit terminase for gp8 because it is located upstream of the terminase gene and because a small number of cluster K genomes have called this gene small subunit terminase. In general, cluster K phage have a single terminase gene called. But a few genomes have a large subunit terminase called (typically gp9) and a small subunit called immediately upstream (gpsmile. The HHPRED results do not match any DNA binding proteins but Phyre2 analysis (see attached) brings back a weak match to a ssDNA binding protein but it is the center portion of the protein (around 13-56) and the predicted structure has two anti-parallel alpha helices. From the literature it looks like its hard to determine crystal structure of small subunit terminase but in general they have an N-terminus DNA binding domain, a center oligomerization domain (two anti-parallel alpha helices) plus C-terminus that interacts with large subunit terminase.

gp8 in other cluster K genomes (e.g. cluster K1 Pixie_smile are of a different pham yet have the same type of matches in Phyre2 (weak matches to ssDNA binding proteins).

Can we go ahead and call these upstream gp8 small subunit terminases and gp9 large subunit terminase or should I go with the old consensus of solely calling the gp9 gene "terminase"?

Thanks!
Sally

| posted 16 Jul, 2019 16:50
I think if the small term or a pham with equivalent phyre predictions is present in every cluster K, it makes sense to designate both as small and large. Are there any that are missing the "small"?
| posted 18 Jul, 2019 10:04
Hi Welkkin,
There are basically two phams for this small subunit terminase in the Ks.

Pham 45539 –> found in all K1, K2, K3, K5, and K6 phage.
Pham46057 –> Found in all K4 and K7 phage
For Pham 45539, small subunit terminase is called for many phage, a total of 62 call it out of 108 . Many don't call it because they are draft but there are 20 non-draft genomes that do not call it

For Pham 46057, there are 15 members total. It is called in only 3 of those genome (of those that do not call it 1 is Malthus and 2 are draft genome).

So perhaps those genes need mass corrections?
 
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