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Showing posts with label Marron. Show all posts
Showing posts with label Marron. Show all posts

Tuesday, 3 July 2012

Connecting B to A

Looking back on the bioinformatic analysis of eukaryotic nitrile hydratases in Marron, Akam and Walker's PLOS One paper to be found here, I thought it would be interesting to look at the link between the two segments which are separate subunits in prokaryotic NHases.
I mocked up this model of where the link had to go from two prokaryotic subunits which had most similarity to the Monosiga brevicollis NHase. The dangling ends of the right hand side of the structure indicate where the linker has to go.

As the easiest to access, I chose to align the protein sequences suggested by the transcriptions of ESTs from the four organisms held within the Broad Institute's Origins of Multicellularity project, namely M. brevicollis, Thecamonas trahens, Salpingoeca rosetta and Sphaeroforma arctica. (NB order in alignment: MB, SR, TT and last SA)

As Marron's paper comments:
"This histidine-rich region is prominent in T. trahens (12 residues), S. arctica (11 residues) and M. brevicollis (17 residues), but shorter in [...] S. rosetta (2 residues)."
That seems quite a lot of variation with only M. brevicollis having a string of pure histidines. In contrast the sequences are around the metal binding segment are quite similar.



Wednesday, 16 May 2012

How widespread are NHases in eukaryotes?

There is a neat diagram summarizing the findings of the paper by Marron, Akram and Walker called "Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups" in PLoS One to be found here in full. There is quite a lot of legend that goes with it that I recommend you look at the paper for, but crucially asterisk * means evidence of one eukaryotic NHase subunit (and hence ** means evidence of both), and hash # means a dodgy read more suggestive of prokaryotic contamination.
So that's a black mark for any NHase in plants and animals then...