SEA-PHAGES | Two piece DnaE-like DNA polymerse III (alpha)

Link to this post \| posted 08 Mar, 2019 22:03
jawsWPI	I'm working on two EF draft genomes. All 7 EF genomes have a DnaE-like DNA polymerse III (alpha) "gene" that has been split into two parts. These are genes 56 and 57 in Anakin and NarutoRun, the genes are coding from different frames (+1 and +2), gene 57's RBS Z score is 2.415 it has a so-so final score of -4.264, and there is a consistent 11 bp gap between the genes. The non-draft genomes AnnaSerena and Krampus give both genes the same DnaE-like DNA polymerse III (alpha) function. In an HHPred anaylsis Gene 56 aa1 - 315 has a 100% probability match to aa 19-324 of an Ecoli DnaE DNA polymerase III (alpha) crystal structure, and gene 57 aa15-594 matches (100% probability) the Ecoli structure from 315 - 1160. (If I run HHPred with the merged gene56+57 sequence I again get a 100% probability match but now to the full length Ecoli crystal structure.) I'm seeing the same split, two pieces with the same function whose summed size "equals" an intact DnaE-like DNA polymerse III (alpha), in non-draft (and by phamerator the draft) genomes of several other small clusters: R, AC, CB, DG, and 2-3 singletons. Not all of the pieces are the same size, and in some cases there is a small, intervening "NKF" gene. The big question is: do I continue the trend and call both functions "DnaE-like DNA polymerse III (alpha)", and if not what is the alternative?

Link to this post | posted 08 Mar, 2019 22:03

I'm working on two EF draft genomes. All 7 EF genomes have a DnaE-like DNA polymerse III (alpha) "gene" that has been split into two parts. These are genes 56 and 57 in Anakin and NarutoRun, the genes are coding from different frames (+1 and +2), gene 57's RBS Z score is 2.415 it has a so-so final score of -4.264, and there is a consistent 11 bp gap between the genes. The non-draft genomes AnnaSerena and Krampus give both genes the same DnaE-like DNA polymerse III (alpha) function. In an HHPred anaylsis Gene 56 aa1 - 315 has a 100% probability match to aa 19-324 of an Ecoli DnaE DNA polymerase III (alpha) crystal structure, and gene 57 aa15-594 matches (100% probability) the Ecoli structure from 315 - 1160. (If I run HHPred with the merged gene56+57 sequence I again get a 100% probability match but now to the full length Ecoli crystal structure.) I'm seeing the same split, two pieces with the same function whose summed size "equals" an intact DnaE-like DNA polymerse III (alpha), in non-draft (and by phamerator the draft) genomes of several other small clusters: R, AC, CB, DG, and 2-3 singletons. Not all of the pieces are the same size, and in some cases there is a small, intervening "NKF" gene.
The big question is: do I continue the trend and call both functions "DnaE-like DNA polymerse III (alpha)", and if not what is the alternative?

Link to this post \| posted 11 Mar, 2019 19:24
cdshaffer	the alternative would be to create two approved annotation terms that indicate how the subdomains of the protein are divided between the two polypeptide chains. This is similar to how some AY phage have the large terminase being split into a "ATP-ase domain" and a "nuclease domain". I think the issue will be is there really value added with defining two new terms. If the split in your DNA pol correlates well with domain locations, like the above terminase example, it might make sense. If, on the other hand, the split does not split nicely domains in a sensible way (like the polypeptides split a doamin into two halves) then there is probably not a better solution than the one currently in use which is to give each part the name of the whole. As a reminder, to propose the addition of the two terms you think would better represent the gene products use the "request a new function" topic.

Link to this post | posted 11 Mar, 2019 19:24

cdshaffer

the alternative would be to create two approved annotation terms that indicate how the subdomains of the protein are divided between the two polypeptide chains. This is similar to how some AY phage have the large terminase being split into a "ATP-ase domain" and a "nuclease domain".

I think the issue will be is there really value added with defining two new terms. If the split in your DNA pol correlates well with domain locations, like the above terminase example, it might make sense. If, on the other hand, the split does not split nicely domains in a sensible way (like the polypeptides split a doamin into two halves) then there is probably not a better solution than the one currently in use which is to give each part the name of the whole. As a reminder, to propose the addition of the two terms you think would better represent the gene products use the "request a new function" topic.

Link to this post \| posted 13 Mar, 2019 15:09
jawsWPI	After some additional digging there is no substantial evidence for two domains in the alpha chain. So, I'm going to continue the trend and leave these two gene calls with the same function. Thanks!

Recent Activity

Two piece DnaE-like DNA polymerse III (alpha)