CHCHD10

[ValWood]

https://www.uniprot.org/uniprot/Q8WYQ3

negative regulation of ATP citrate synthase activity ATP biosynthetic process

Is MICOS subunit Mic14. https://www.ncbi.nlm.nih.gov/pubmed/?term=CHCHD10+micos When this is curated (good reviews for the entire complex are listed here: https://github.com/geneontology/go-ontology/issues/15245

existing annotations should be reviewed seem to be indirect phenotypes due to mitochondrial disfunction in micos mutants (not related to functional role for MICOS)

[ValWood]

Hi Penelope,

Could you pass this one to the appropriate GOA person.

Thanks

Val

[pgarmiri]

Hi @ValWood ,

I finally got some time and had a look at this protein.

I curated one of the papers you suggested (PMID: 26666268 ). The other one was more about the disease causing variant of the protein. I added another one that was done mainly with the mouse protein that would provide new annotations ( PMID:28585542 "Loss of function CHCHD10 mutations in cytoplasmic TDP-43 accumulation and synaptic integrity.")

Regarding the existing annotations you pointed out. They are not indirect phenotypes but rather indicators for involvement in processes relevant to the protein.

1. ATP is the final product of the OXPHOS system. They had experimental conditions to study that in that paper. They cultured the cells in glucose-free medium supplemented with galactose cellular ATP-synthesis is largely restricted to the OXPHOS system. This stands for Oxidative Phosphorylation (UK /ɒkˈsɪd.ə.tɪv/, US /ˈɑːk.sɪˌdeɪ.tɪv/)[1] is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing energy which is used to produce adenosine triphosphate (ATP). (https://en.wikipedia.org/wiki/Oxidative_phosphorylation#Cytochrome_c_oxidase_(complex_IV)). They found that "HELA-cells transfected with siRNA against CHCHD10 or SURF1 displayed a significant reduced total ATP-level under all experimental conditions".

So, I would suggest to delete the annotations to GO:0006754 'ATP biosynthetic process' as it seems a bit redundant when an annotation to GO:0006119 'oxidative phosphorylation' is already present.

2. The authors also say "We observed an increase in citrate synthase activity in the GBAS and CHCHD10 knockdown cells, indicating an increased mitochondrial biogenesis in both series."

I think that would lead to an annotation to GO:0007005 'mitochondrion organization' instead of 'negative regulation of ATP citrate synthase activity'.

Definition of GO:0007005 'mitochondrion organization' : A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.

3. I have added one more annotation based on what the authors found "CHCHD10-knock-down indeed leads to a reduced complex IV activity" (Complex IV, also called cytochrome c oxidase, is the terminal component of the respiratory chain.)

GO:1904960 'positive regulation of cytochrome-c oxidase activity'

4. I would also delete the ND annotation for the Molecular Function as the interaction are with members of the MICOS complex.

These annotation were added by BHFL (in 2012), so I can't edit them. If you are happy with my suggestions, we can tag the relevant person or they can be disputed in Protein2GO.

Let me know what do you think.

Thanks,

Penelope

[RLovering]

Hi Penelope

I spotted this in my inbox. I have deleted 2 of the annotations for you. But I didn't realise it has been agreed that protein binding data is sufficient to remove ND MF annotations. Or as it is part of the the MICOS complex are you planning to add an activity based on its function here? Thanks Ruth

[pgarmiri]

Hi Ruth,

Thank you for looking into those so promptly! Would you be happy with changing the other proteins as well? I think the same arguments above are valid for all proteins curated.

My suggestion was not to just delete the 'negative regulation of ATP citrate synthase activity' but to replace it with GO:0007005 'mitochondrion organization' ( ..that experiment was indicating an increased mitochondrial biogenesis in both series). As for the ND you are right, there was no final decision on that. I meant that it was not just a random interaction but a real one leading to the MICOS complex. Thanks, Penelope

[RLovering]

Hi Penelope

sorry I should have spent more time reading your comments. All done I think

Best

Ruth

[ValWood]

All the evidence so far for MICOS affecting oxidative phosphorylation appears to be indirect (due to the affects on inner membrane morphology). Summarized nicely in this recent review https://www.ncbi.nlm.nih.gov/pubmed/27245231 I wouldn't annotate MICOS to oxidative phosphorylation.

This indeed appears to be the case. Mic60 depletion affects Δψ and ATP production (Ding et al. 2015; John et al. 2005). Levels of mitochondrial respiratory complexes I and IV are diminished after a prolonged knockdown of Mic60 (Ott et al. 2012). The defects in the respiratory complex IV assembly have also been connected to mutations in Mic14 (Genin et al. 2016), and the depletion of Mic13 was found to affect mitochondrial respiration (Guarani et al. 2015). The knockdown of Mic19 causes significant defects in energy production—the oxygen consumption and lactate production are drastically decreased, although the ATP levels are moderately affected. In addition, the levels of two components of the respiratory complex IV are affected by the Mic19 depletion (Darshi et al. 2011). Furthermore, both overexpression and downregulation of Mic27 and Mic23/Mic26 have negative effects on mitochondrial respiration (Koob et al. 2015). Mic27 also binds to cardiolipin, a lipid necessary for the organization of respiratory chain complexes (Weber et al. 2013).

Interestingly, the knockdown of the MIB component Sam50 decreases respiratory complexes I and IV levels and, after a prolonged depletion, also complex III and F1FO-ATP synthase levels (Ott et al. 2012). The observation that the knockdown of Sam50 strongly affects the cristae structure, but not the levels of the MICOS components (Ott et al. 2012, 2015), indicates that this effect on respiratory complexes is probably due to the changes in the inner membrane morphology, which in turn might be connected to mtDNA stability. However, we observed that the depletion of Sam50 or Mic60 leads to a reduction of the respiratory complex IV assembly factor RESA1/Coa7 (Kozjak-Pavlovic et al. 2014), as well as of TTC19 (unpublished results), a respiratory complex III assembly factor (Ghezzi et al. 2011). Therefore, it is possible that the cause of respiratory complex defects in the mitochondria depleted of the MICOS and MIB components is the diminishing of the intermembrane space assembly factors combined with mtDNA instability.

[pgarmiri]

Hi @ValWood ,

I am afraid I don't have access to the paper you pointed, so I can read only the abstract and the parts you posted here. So, just from those I understand that certain component of MICOS are required for the formation and function of certain respiratory complexes (the last two sentences above).

Also, I found this paper (work done in yeast) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434539/ They say "As part of the approach to understand MICOS complex organization, Friedman et al. removed the six MICOS proteins from yeast cells. Inside these cells, the inner mitochondrial membrane was misfolded. Furthermore, the respiratory complexes did not work normally and as a consequence the cells were unable to grow normally, suggesting that the correct distribution of respiratory complexes in the inner membrane is important for ATP production and depends on MICOS."

Wouldn't those potentially indicate an upstream involvement in 'oxidative phosphorylation' rather that just a side effect?..or even 'regulation of ..'?

[ValWood]

Hi Penelope,

Apologies for the delay. I still think this is indirect.

based on this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434539/ The membrane is not folded correctly and so the distribution of the ATPase complexes is affected. I would not annotate MICOS to GO:0006119 'oxidative phosphorylation'

Pretty much most of the mitochondrial proteins will affect some aspect of oxidative phosphorylation The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.

but this should be reserved for the energy generators themselves: e.g. https://www.pombase.org/term/GO:0006119

Based on the guidelines I would not make this annotation http://wiki.geneontology.org/index.php/Annotating_from_phenotypes (Similarly I would not annotate 'assembly of respiratory complexes' to the energy generation terms either, even though they give this phenotype)

The term which could be annotated is

GO:0007006 mitochondrial membrane organization or GO:0042407 cristae formation

Incorrect cristea formation results in mislocalized respiratory machinery. It is 'required for normal' respiration but not directly "involved in". 'regulation' oxidative phosphorylation would not be correct either because if everything was working correctly this would not 'control' this pathway.

[pgarmiri]

Hi Val,

Sorry for replying only now but I was back only on Friday and slowly catching up with pending issues.

• I see your point of why the 'regulation of' or 'involved_in' is not the right way to go here. GO:0007005 'mitochondrion organization' has already been added based on the paper, so the annotation to GO:0006119 'oxidative phosphorylation' should be just removed?

• I have another question for another annotation I added that I would like your input , please.

On PMID:26666268 they found that the expression of CHCHD10 mutant alleles inhibits apoptosis by preventing cytochrome c release (I have added GO:0090200 'positive regulation of release of cytochrome c from mitochondria' based on this)

Based on PMID:20888800 I had added one more annotation GO:1904960 'positive regulation of cytochrome-c oxidase activity'

(Authors found that "CHCHD10-knock-down indeed leads to a reduced complex IV activity" (Complex IV, also called cytochrome c oxidase, is the terminal component of the respiratory chain.)

Now reading the thread again, I have a feeling that that might be considered as indirect as well? Or perhaps the 'acts_upstream _of' qualified could be used as the complex first needs to be released from the mitochondria to be able to perform its function?

Thanks,

Penelope

[ValWood]

Yes I agree, I think all of these are only readouts and phenotypes.

I notice I have annotated the fission yeast protein to aerobic respiration (from ISS to SGD). However, this is only a phenotype too (many mitochondrial mutants have decreased respiration). Normally I would not make this annotation, so I am going to remove this and reclassify just as "mitochondrial protein" for fission yeast-an "unknown process" annotation is more useful here. I checked to see if there were more recent papers for yeast or human and I could not find anything.

@pgaudet thoughts?

[pgarmiri]

Hi Val, I removed those two annotations. The good thing is that there were evidence for other annotations that I think are more meaningful, like:

GO:1901030 'positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway' and GO:1903852 'positive regulation of cristae formation'

Thanks,

Penelope

[ValWood]

OK. The human and mouse proteins still look overannotated in UniPRot, but hopefully these will resolve in future when we have more experimental detail.

I'll close this for now. Possibly more later... v