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respiratory complex assembly/ respirasome assembly #3
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This is great. I have a rough but incomplete list of assembly factors. I will start putting them in some order. |
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Notes
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@hattrill should "NOT SEEN" be in the final column for the ones below NDUFAB1 (I am assuming this always means that it isn't in my list?) |
Hi @ValWood there are quite a few that I have doubts about - some are modifiers and protein maturation factors that have made their way onto HGNC, MitoCarta or via GO - IBA, ISS, etc. As this is a mash-up of HGNC calls, MitoCarta calls and what we have in the GO, think there will be a lot of removal from this. We have COX6B1 as a MITOCHONDRIAL COMPLEX IV - SUPERNUMERARY SUBUNIT gene groups. - I've made a note about those as many of the supernumerary/accessory subunits have assembly GO terms - I think that this is because they are required for complex stability rather than assembly and it's 'cellular phenotype that's been annotated. That's why need to align it against reviews. "NOT SEEN" means that I found an ortholog via DIOPT for Pombe but not on your list (or I could have missed when I did the cross-search. Human ATPSCKMT, FDXR, FDX2, HCCS, LRPPRC, OXA1L, SCO1 - come from HGNC or MitoCarta are ones on my current 'dump' list as they seem upstream to assembly. |
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Hopefully fixed now - some columns got merged a messed the layout up. I will be removing a lot from the list....just trying to work out where to start - think that ones that are classed as accessory/supernumerary subunits will be first stop there are a lot. |
OK once you have cleaned up, I'll review the pombe ones and make sure all of mine are in your table. I'll also have a good look for anything that is missing from pombe (although I am not expecting to find the Complex I assembly - because we don't have it). We do have 3 (I think ) of the subunits but these might really be assembly factors that are also used by other complexes (or something like that). |
This looks like a nice review publication to start with for me: |
The Wikipedia page isn't half bad, I was looking at it the other week when I found some of the assembly factors in pombe |
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Think I've found the paper that 'poisoned' the complex I assembly well - A lot of annotations originate from PMID:27626371 in which the KO of different accessory CI SUs were examined for their role in assembly. However, although the absence of SUs may impact assembly, I think that this is because they have a structural role in the complex/complex intermediates rather than being factors that assist in the assembly of the complex. I like this as a definition of assembly "This multistep process involves transiently associated assembly factors that integrate core and accessory/supernumerary subunits as well as cofactors into the final holoenzyme." (PMID: 38086790). I will have a bit more of a dig and then ask Alex Whitworth as if this works need to get a few places to revise their lists as well as GO. |
Think that list is ok now - will take a bit for GO fixes to filter down.
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We do have bona fida orthologs of COA1 (coa1 https://www.pombase.org/gene/SPBC16E9.03c NDUFAF1 https://www.pombase.org/gene/SPAC9E9.15 TTC19 https://www.pombase.org/gene/SPAP27G11.02
These don't get picked up by the ortholog predictors but are clear from directed searches using Jackhmmer/FoldSeek/Pfam-N etc |
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Also, looks like we don't have an ortholog for SDHAF1 (Human), which is SPAC664.12c in Pombe |
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FIXES
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Woah, https://www.uniprot.org/uniprotkb/Q96E52/entry is over-annotated CC @Antonialock |
Disputed some assembly annotations to human ones...and a special request for a big batch from PMID:27626371 |
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INteresting.
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