Pathway: cardiolipin metabolic process (we have a floater!)

[ValWood]

@Antonialock 's first GO-CAM!

The model
http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A67086be200000363

The genes
https://www.pombase.org/results/from/id/3cf1abdc-1a95-4603-a17d-26f84425bfb8

Systematic ID	Gene name	Product description	Budding yeast orthologs	Human orthologs
SPBC26H8.11c	the4	acyl-coenzyme A thioesterase The4	MRX3	THEM4,THEM5
SPAC22A12.08c	crd1	cardiolipin synthase/ hydrolase fusion protein Crd1	CRD1,YKR070W	CRLS1,HDHD5
SPBP18G5.02	pgs1	CDP-diacylglycerol-glycerol-3-phosphate3-phosphatidyltransferase Pgs1	PGS1	PGS1
SPAC6G10.03c	cld1	mitochondrial cardiolipin-specific phospholipase Cld1	CLD1	ABHD4,ABHD5
SPBC1A4.06c	tam41	mitochondrial phosphatidate cytidylyltransferase Tam41	TAM41	TAMM41
SPCC645.02	gep4	phosphatidylglycerol phosphate phosphatase Gep4	GEP4

Issues
Unable to connect the4

[ValWood]

• Fungal GEP4 has a functional ortholog but not true ortholog, I can't remember which phosphatase it was, we will dig that out
• Also @Antonialock the situation with taffazin, which is missing from pombe might be similar to GEP4, perhaps replaced by a non orthologous gene?

[Antonialock]

• Fungal GEP4 has a functional ortholog but not true ortholog, I can't remember which phosphatase it was, we will dig that out

"Our results indicate that PTPMT1 orthologs from both Drosophila and bacteria serve as functional equivalents of GEP4 in yeast"
https://pmc.ncbi.nlm.nih.gov/articles/PMC3576122/

our results demonstrate that mammalian PTPMT1 serves as a functional equivalent of GEP4 in yeast (Figure 6E).
(mouse)
https://pmc.ncbi.nlm.nih.gov/articles/PMC3119201/

[Antonialock]

"It is even questionable whether S. pombe de novo synthesized CL undergoes a FA remodeling process as there is no obvious tafazzin ortholog in this yeast (PomBase). Even though the S. pombe SPAC6G10.03c ORF is annotated in the PomBase as a mitochondrial cardiolipin-specific phospholipase Cld1 based on sequence homology with S. cerevisiae CL specific phospholipase Cld1 (Baile et al., 2014; Beranek et al., 2009), the product of the SPAC6G10.03c ORF is not involved in the CL remodeling process. Firstly, the product of the SPAC6G10.03c ORF does not localize to mitochondria (Matsuyama et al., 2006). Secondly, FA analysis of the SPAC6G10.03c deletion strain showed no difference between the wild-type strain and the strain with deletion of SPAC6G10.03c; this is something that would be expected if this potential phospholipase plays a role in the CL remodeling process (unpublished results)."

https://onlinelibrary.wiley.com/doi/full/10.1002/yea.3451

[ValWood]

Thats a useful review. @PCarme could you add to you list to take this review and add any other phospholipid pathways from this?

[Antonialock]

Is this positive regulation of CL biosynthesis/ just plain CL biosynthesis (without the regulation prefix ) + inner mitochondrial membrane organization?

Mieap drives formation of biological condensates (membrane less organelles, MLOs) involved in cardiolipin metabolism. Mieap BCs specifically phase separate the mitochondrial phospholipid, cardiolipin. Mieap directly binds to cardiolipin in vitro. Lipidomic analysis of cardiolipin suggests that Mieap promotes enzymatic reactions in cardiolipin biosynthesis and remodeling. Accordingly, four cardiolipin biosynthetic enzymes, TAMM41, PGS1, PTPMT1, and CRLS1 and two remodeling enzymes, PLA2G6 and TAZ, are phase-separated by Mieap BCs.

https://pmc.ncbi.nlm.nih.gov/articles/PMC10845071/

[ValWood]

Is this positive regulation of CL biosynthesis/ just plain CL biosynthesis (without the regulation prefix ) + inner mitochondrial membrane organization?

There is a lot to pick apart here!

My knowledge about mieap is limited d to its role in nquality control
i.e.
Mieap, a p53-Inducible Protein, Controls Mitochondrial Quality by Repairing or Eliminating Unhealthy Mitochondria
https://pmc.ncbi.nlm.nih.gov/articles/PMC10845071/

Is this really demonstrating involvement in cardiolipin biosynthesis? It isn't clear to me.

They say
Mieap has been reported to form vacuole-like structures, designated as Mieap-induced vacuoles (MIVs).31 To confirm this hypothesis, we performed the IF experiment on structures comprising EGFP-Mieap. EGFP-Mieap reproducibly formed green condensates, while antibodies (anti-Mieap antibody and anti-GFP antibody) produced ring-shaped staining around the green condensates (Figure S1A). Thus, we suspected that antibodies are unable to permeabilize EGFP-Mieap condensates.

Mieap condensates exhibited spherical or oval shapes, fusion, and multi-phase structure consisting of two phases: a Mieap-containing phase and a Mieap-depleted phase (Figures S1A, S1C, S1D, and Video S1). These characteristics, and their propensity to fuse, are not contradictory to a notion that Mieap condensates have liquid-like properties, suggesting that these structures are droplets.3 Therefore, we designate Mieap-induced structures as Mieap BCs (Mi-BCs).

They say there is cardiolipin in the structure, so presumably it does have some membrane properties, so are they condensates, or membrane bound?

These is also information about :
Mieap prevents obesity by maintaining cristae structures of BAT
presumably affecting mitochondrial membrane would also affect lipid metabolism and hence cardiolipin, but it this a regulatory mechanism, I'm not sure it is possible to know from this paper?

"In the current study, we have demonstrated a possible model of MLOs involved in CL biosynthesis and remodeling in over-expression experiments with various fluorescence-tagged proteins. However, we have not yet showed a real picture of physiological Mi-BCs in vivo. Utilizing newly developed technologies for imaging, physiological Mi-BCs must be explored and demonstrated in future study. For this purpose, it is important to establish mNeonGreen-Mieap knock-in mice to analyze endogenous Mieap protein. Furthermore, it is also critical to show that artificial Mi-BCs really contain CL metabolic enzymes and substrates/intermediates and that CL enzymatic reactions are promoted in Mi-BCs in the next study.'

I would say this is too hypothetical for GO curation right now.....

[ValWood]

ACTIONS

• cld1 NOT GO:0032048 (cardiolipin metabolic process) PMID:3011744 TAS
• the4 NOT GO:0032048 (cardiolipin metabolic process) PMID:3011744 TAS
  cld1 NOT GO:0005739 (mitochondrion) PMID:3011744 TAS
  (i.e made the "NOTs" as generic as possible
• removed GO:0035965 (cardiolipin acyl-chain remodeling) from the4 & cld1
• removed GO:0007006 (mitochondrial membrane organization) IC with cardiolipin metabolic process from cld1
• Cld1 product updated, (it's a shame about the name, but we won't change it unless requested)
• cld1 and the4 were deleted from the GO-CAM model for cardiolipin metabolism.
• still need to remove the PAINT propagation, will do that tomorrow when I can see if any filtered ones re-appear.