I have removed the pathway from the S.cerevisiae and S.pombe proteins, which triggers the GO term. This will for now solve the issue of the seemingly conflicting GO terms coming from this pathway to the ones assigned by you and SGD to these proteins.
That said, I'm not entirely convinced by these terms assigned. While it has been shown that Mns1 is required for proper degradation of misfolded glycoproteins from the ER, it actually catalyses the trimming of the terminal mannose residue irrespective of the folding state of the protein. It does so also on properly folded proteins that leave the ER to the Golgi for further processing, and orthologs have also been shown to do so in human and plants, so it can actually be considered part of the normal maturation pathway of glycoproteins (hence the initial assignment to the pathway in UniProt I guess).
It's requirement for degradation is rather due to the fact that the Pdi1-Mnl1 mannosidase complex - which actually generates the signal for degradation of unfolded proteins by further trimming of the carbohydrates - only accepts the Mns1-processed Man(8) and not the precursor Man(9) as substrate.
We will therefore not create a pathway for degradation/deglycosylation, as it is extremely difficult to define the starting point of such a pathway.
Best,
-ivo
Last edit: ivo 2014-09-24
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Sent to UniProt.
Thanks for having pointed out this error.
I have transferred it to Ivo & Marc
Cheers,
Anne
Last edit: Anne Morgat 2014-09-24
Hi Val,
I have removed the pathway from the S.cerevisiae and S.pombe proteins, which triggers the GO term. This will for now solve the issue of the seemingly conflicting GO terms coming from this pathway to the ones assigned by you and SGD to these proteins.
That said, I'm not entirely convinced by these terms assigned. While it has been shown that Mns1 is required for proper degradation of misfolded glycoproteins from the ER, it actually catalyses the trimming of the terminal mannose residue irrespective of the folding state of the protein. It does so also on properly folded proteins that leave the ER to the Golgi for further processing, and orthologs have also been shown to do so in human and plants, so it can actually be considered part of the normal maturation pathway of glycoproteins (hence the initial assignment to the pathway in UniProt I guess).
It's requirement for degradation is rather due to the fact that the Pdi1-Mnl1 mannosidase complex - which actually generates the signal for degradation of unfolded proteins by further trimming of the carbohydrates - only accepts the Mns1-processed Man(8) and not the precursor Man(9) as substrate.
We will therefore not create a pathway for degradation/deglycosylation, as it is extremely difficult to define the starting point of such a pathway.
Best,
-ivo
Last edit: ivo 2014-09-24
I agree, it seems that your mapping was OK.