Pathway: oxidative phosphorylation (GO:0006119)

[ValWood]

Pathway: oxidative phosphorylation (GO:0006119)

Complete gene set https://www.pombase.org/term/GO:0006119

The model is missing the proton-transporting ATP synthase complex (GO:0045259)/ proton motive force-driven mitochondrial ATP synthesis (GO:0042776) sub-part

because I don't have a COmplex Portal ID for proton-transporting ATP synthase complex (GO:0045259) https://www.pombase.org/term/GO:0045259 (I could add it with the complex sub-parts) See https://github.com/geneontology/go-ontology/issues/29067

Model Link: http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A663d668500000596

Current Model:

GOCAM viz

GOCAM viz complexes uncollapsed

[ValWood]

If we agree this is the way to model this process, the fly pathway should be identical, except ndi1 will be substituted by complex I

[ValWood]

@Antonialock

[hattrill]

Yikes - think if we are having to add components by has_part we could do with a bulk upload method....For complex I I have 44 members!

[hattrill]

Building the Fly version - not connected anything or filled in all the gaps yet: http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A67086be200000314

[hattrill]

Added some connections - think will have to add H+ input to complex V and add Cytochrome c and electron transferring flavoproteins somewhere in the mix

[hattrill]

Adding this note: CHEBI has electron entry....CHEBI:10545

[ValWood]

Yikes - think if we are having to add components by has_part we could do with a bulk upload method....For complex I I have 44 members!

That's why this ticket should be a priority, please add your voice! https://github.com/geneontology/noctua/issues/905

[ValWood]

Added some connections - think will have to add H+ input to complex V and add Cytochrome c and electron transferring flavoproteins somewhere in the mix

If you can add these parts I will copy them.

I will try to rationalize the assembly factors (I'll open a separate ticket) we have a good start https://www.pombase.org/results/from/id/e5831c48-bd63-425d-92b1-c9dcd8aad95e but there is some slightly wonky ontology ). I want to find out if these are really all assembly factors and, if so, what (i.e. chaperone) - some have turned out to be stabilizing the mRNA, so assembly is just a phenotype; this will take a while because I'm busy next week or so.

[ValWood]

~PomBase Tim18 has GO:0020037 heme bindingIBA with PTN001000243 , A5GZW8 GO_REF:0000033 19 GO:0048039 ubiquinone bindingIBA with A5GZW8 , PTN001000243 GO_REF:0000033 2~ ~which looks incorerct for this subunit. @Antonialock coud you check this? (I think its from the complex)~

@tim18 ignore- it has binding sites!

[hattrill]

1. Modified to show H+ output/input from complexes to complex V
2. Added cyt c
3. Very roughly added ETF complex and Etf-QO as place-holders - they mediate e- transfer from other mitochondrial pathways to ubiquinol for input for complex III. PMID: 33450351, but do not know what BP to add here as where boundary on oxphos chain is is unclear to me just now.

[ValWood]

Systematic ID	Gene name	Product description	Budding yeast orthologs	Human orthologs	Fly
SPAC27D7.06	etf1	electron transfer flavoprotein alpha subunit EtfA	AIM45	ETFA	wal
SPAC1805.02c	etf2	electron transfer flavoprotein beta subunit EtfB	CIR1	ETFB	Etfb
SPAC20G8.04c	cir2	mitochondrial electron transfer flavoprotein-ubiquinone oxidoreductase Cir2	CIR2	ETFDH	Etf-QO

[ValWood]

@hattrill says The electron transfer flavoprotein complex is formed from: FBgn0010516 walrus wal FBgn0039697 Electron transfer flavoprotein beta subunit Etfb Had to just use a table of SUs for this: PMID:15693940 It's not really part of the OXPHOS chain but is a link between things like beta oxidation feeds electrons via FBgn0286783 Etf-QO Electron transfer flavoprotein-ubiquinone oxidoreductase to CIII

@hattrill are there 2 complexes formed by these 3 proteins?

[hattrill]

Think comment I answered was associated with the assembly ticket:

The electron transfer flavoprotein complex is formed from: FBgn0010516 walrus wal FBgn0039697 Electron transfer flavoprotein beta subunit Etfb

Had to just use a table of SUs for this: PMID:15693940

It's not really part of the OXPHOS chain but is a link between things like beta oxidation feeds electrons via FBgn0286783 Etf-QO Electron transfer flavoprotein-ubiquinone oxidoreductase to CIII

I am not sure whether to model it as beta ox as it is prob a general e- transfering thing for other processes....but think that might become clearer when other processes are tackled

[hattrill]

As far as I know, the EFT is just these two: FBgn0010516 walrus wal FBgn0039697 Electron transfer flavoprotein beta subunit Etfb

http://www.ebi.ac.uk/interpro/entry/InterPro/IPR033947/ says The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer."

[hattrill]

I haven't made a CP entry for EFT yet, as I have parked it as I wasn't quite sure which process it belongs to or whether it just sits between processes

[ValWood]

CHATGPT says

Yes, human ETFA, ETFB, and ETFDH are components of the mitochondrial electron transfer flavoprotein complex (ETF). They work together to facilitate the transfer of electrons from specific flavoprotein dehydrogenases to the respiratory chain via electron transfer flavoprotein oxidoreductase (ETF-QO).

Breakdown: ETFA (Electron Transfer Flavoprotein Alpha): The alpha subunit of ETF. ETFB (Electron Transfer Flavoprotein Beta): The beta subunit of ETF. ETFDH (Electron Transfer Flavoprotein Dehydrogenase): A flavoprotein that serves as an intermediary, receiving electrons from ETFA/ETFB and transferring them to the ubiquinone pool in the mitochondrial inner membrane.

so it seems that all 3 are involved...

Also, These proteins collectively form part of the electron transfer flavoprotein system, which is crucial for fatty acid β-oxidation and the catabolism of some amino acids. The ETFA and ETFB subunits form the heterodimeric ETF protein, while ETFDH connects this system to the respiratory chain.

[hattrill]

Ok, that makes sense.

[ValWood]

I bunged them in my model so I don't forget , will connect them up later

[hattrill]

That's kind of what I did - you have reminded me of it now!