AAA proteins are ATPases associated with various cellular activities. They have two ATPase domains containing Walker A and Walker B consensus sequences called D1 and D2 domains, and an N-terminal domain that is more variable. The AAA proteins usually form hexameric ring-like molecules and are involved in mechanic cellular work.
One of the AAA proteins that is studied in the lab is N-ethyl maleimide sensitive factor (NSF). This protein is involved in vesicle fusion and is thought to function by breaking apart the SDS resistant SNARE complexes. Although NSF have two ATPase domains only one of these catalyse ATP hydrolysis effectively. The ATPase defective domain is instead involved in forming the hexameric ring structure.
NSF is a conserved protein with homologues in many organisms. Drosophila melanogaster have two proteins that are homologous to NSF, called NSF/comatose and NSF2. The two dorsophila NSFs are expressed differentially during development but people have thought that maybe humans have two isoforms of NSF too. To investigate if there is another NSF homologue NSF was blasted against the predicted genes from the latest ENSEMBL golden path (some time in April 2001). No novel close homologues were pulled out of the database.
By looking at the sequence homology between proteins it is possible to infer phylogenetic / evolutionary relationships between the proteins. Therefore I found the protein sequences of NSFs from different organisms and did a multiple sequence alignment using CLUSTALW. The multiple sequence alignment (MSA) come with a phylogenetic tree that is pretty accurate. To get a more accurate phylogenetic tree the MSA was fed to the program PHYLIP, which makes good phylogenetic trees.
To get an evolutionary tree of the organisms the taxonomy browser at NCBI was used. From the MSA tree it seems like the change from one NSF isoform to two happened in the insects only. Comparing the two trees show that the MSA tree correlate very well with the actual evolutionary tree.
It is off course not possible to rule out the possibility that there is two NSFs in other organisms based on these data alone.
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