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#11348 NTR - response to depolarised mitochondrion
closed-fixed
5
2015-02-13
2014-11-25
No
NTR - response to depolarised mitochondrion
Induction of mitochondrial depolarisation with a non-physiological compound CHEBI: 75458 (“CCCP"), causing most mitochondria in a cell to become depolarised, leads to significant, easily detectable levels of mitophagy (GO:0000422 mitochondrion degradation). Many experiments require use of this or related chemicals and various gene products modulate or are required for responses to the resulting depolarised mitochondria e.g. PMID_ 21855797, PMID_ 25215947.
Because it is non-physiological, I cannot capture use of this chemical in a term or in column 16, but it would be useful to be able to annotate using a new term, “response to depolarised mitochondrion”, that is one of the downstream processes resulting from CCCP treatment.
I think this would be child to
GO:0033554 cellular response to stress
?
Examples of proteins that would be annotated using this term are:
Parkin (PARK2) O60260
AMBRA1 Q9C0C7
GOC:ref
GOC:pad
Hi Paul,
To recap, the CCCP assay is used to uncouple mitochondrial membrane potential, make the inner mitochondrial membrane permeable, and often ultimately induce apoptosis (see http://www.abcam.com/cccp-ab141229.html). If CCCP were a gene product, its function would be GO:0017077 oxidative phosphorylation uncoupler activity. CCCP treatment, when coupled with overexpression of PARKIN, induces mitophagy. However, it appears to be debatable whether this entire pathway (your “response to depolarised mitochondrion”, or possibly, in GO speak, ‘mitophagy in response to mitochondrial depolarization’) can be considered physiological or not: the second paper you quote says: “Hitherto, in mammalian cells, overexpression of PARKIN in combination with CCCP treatment is the only known method to induce mitophagy.”
There has been recent discussion within the GO Consortium resulting in a proposal to capture assays in the With column using the OBI (Ontology for Biomedical Investigations). This hasn’t been ratified yet, but the rationale is that we should annotate to the ‘real’ process for which researchers use substitute assays (e.g. electrophysiologists use rubidium to measure ability of membranes to transport potassium; the real process is ‘potassium transmembrane transport’). My problem here is that I’m not sure what the real process would be. Would one of the following existing terms capture the roles of Parkin and AMBRA1?
GO:0051882 mitochondrial depolarization
GO:0007007 inner mitochondrial membrane organization
GO:0035794 positive regulation of mitochondrial membrane permeability (we could create a child GO:NEW mitochondrial inner membrane permeabilization)
GO:0000422 mitochondrion degradation (or one of its children)
You may want to ask for Becky’s opinion too.
Thanks,
Paola
This sound indirect to me (would be better captured as a phenotype than a process)
In response to Paola, mitophagy is observed in absence of external inducers, but only in a tiny minority of cells.
Ways in which mitophagy can be induced in mammals, other than by compounds like CCCP, include mitochondrial DNA damage (PMID: 20547844) and photo-irradiation (PMID: 21126216). Neither really “physiological”; the DNA damage requires over-expression of Parkin and the photo-irradiation model uses 488-nm light shone on individual mitochondria, which are then selectively removed by mitophagy. However, there are variations of mitophagy that are developmentally regulated and do not require chemical / physical induction - e.g. red blood cell precursors have their mitochondria removed by selective mitophagy, but the triggering event or molecule(s) is unknown (reviewed in PMID_22743996).
Parkin is NOT absolutely required for mitophagy - expression of AMBRA1, when targeted to mitochondria, together with CCCP treatment, induces mitophagy (PMID_25215947).
Val - sorry, being relatively new to GO, how would I capture a phenotype in GO? Do you mean using something like an external ontology such as the Phenotype and Trait Ontology (PATO) ?
Hi Paul,
It seems to me that "response to depolarized mitochondria" isn't a normal biological process. Probably it wouldn't be a phenotype annotation either, or the phenotype would be
"depolarized mitochondria" and the condition would be "CCCP", but as far as I'm aware there is not phenotype ontology or phenotype annotation system in place for human.
This does not sound as though it is
"regulation of membrane permeability" there is no regulation the chemical insult is being used to generate an experimental scenario. I also don't think that "response to depolarized mitohondria" would be a term we would usually create? This seems to be an experimental technique to
induce mitophagy?
It might also be useful to get Pascale's input here as she has good guidelines for what is considered and experimental readout. To me these terms seem outside the normal scope of GO. The GO processes should reflect a gene products normal activity.
Hello Paul,
Looking at the two papers (PMID_ 21855797, PMID_ 25215947), my opinion is that the CCCP treatment seems to be part of the experimental procedure rather than the process being looked at. I would personnally recommend that you annotate to mitophagy, which is what 'mitochondrial clearance' is in this context.
Thanks,
Pascale
Thanks all for your feedback - makes very good sense to me.
Paul, would you be happy to follow Pascale's advice? Or if you have any questions left, please feel free to ask.
Thanks,
Paola
Note for self: also see related request
https://sourceforge.net/p/geneontology/ontology-requests/11291/
Hi Paola
happy with feedback from Val and Pascale and I was already using a child of GO:0000422 mitochondrion degradation, BUT I haven't explained well enough what I want to do - I would argue that CCCP (or FCCP) is mimicking or amplifying the normal process of depolarisation, based on mitophagy in reticulocytes:
Mitochondria become depolarised prior to mitophagic clearance in wild-type mammalian reticulocytes as part of the normal process of differentiation e.g. PMID: 18454133, PMID:20080761, in the absence of any exogenous chemicals /inducers such as FCCP or CCCP.
Also, a normal human peptide, smARF (an alternative translation product of the CDKN2A gene - PMID:25217637) stimulates mitochondrial depolarisation and subsequent PINK1/Parkin-dependent mitophagy; again, in absence of chemical inducers.
Mitochondrial depolarisation seems to be necessary for mitophagy (at least in red blood cell precursors), because a block on mitophagy caused by knockout of Nix (Q9Z2F7 - (PMID: 18454133)) is relieved if treat reticulocytes with FCCP (FCCP abolishes mito. membrane potential) or a compound called ABT-737 (PMID:15902208 - described as “a BH3 mimetic”).
I’m not trying to capture the depolarisation itself (we already have GO:0051882 mitochondrial depolarisation), but the physiological response to depolarisation.
One example of use would be that parkin is selectively recruited or translocated to depolarised mitochondria prior to mitophagy (PMID:19029340). If I simply annotate parkin is part_of mitochondrion GO:0005739 and is part_of mitophagy GO:0000422 mitochondrion degradation, I am not capturing richness of experimental detail. How can I indicate that parkin is only, or mainly translocated to depolarised mitochondria?
I think we would do
Parkin mitochondria occurs_during(mitophagy)
to capture when the localization occurs
Hi Paul,
Hopefully, Val's latest comment was helpful to you. Please let us know if you feel that further discussion is needed. Also, I see that this related ticket was closed recently, so I was wondering if we could consider this one as done too?
https://sourceforge.net/p/geneontology/ontology-requests/11291/
Thanks,
Paola
Hi all,
I'm working on a related ticket for Paul: https://sourceforge.net/p/geneontology/ontology-requests/11456/
From reading the references on that ticket it seems to me that, like DNA damage, poorly functioning mitochondria with reduced membrane potential are a normal part of life with a specific pathway devoted to flagging and cleaning up the damage. The confusion comes from the fact that many experimental investigations of this pathway involve artificial induction of mitochondrial damage. But this is no different to the way response to DNA damage is investigated. I'd like to add the term requested here to use it in defining a term for the above ticket.
I'd like to get this wrapped up this week, so will go ahead unless I hear any objections in the next day or two.
Cheers,
Davd
Draft of new term:
label: "response to reduced mitochondrial polarisation"
definition: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting on a mitochondrion, resulting in reduced polarisation of the mitochondrial membrane."
I don't know, David - I can see your rationale, and I accept that this may represent a 'physiological' condition, but I am uncomfortable with the label you suggest, as it carries reminiscences of non-GO ontologies. Based on your proposed def, I'd go for some sort of 'response to mitochondrial stress' results_in 'neg reg of mitochondrial membrane polarization'? Sorry, I don't have a chance to look at this in more detail now, but I'd suggest you wait to hear if at least Val and Pascale (and David H who had a related ticket) have any alternative suggestions.
Thanks for researching this, however. It is a very relevant area in neurodegeneration.
Paola
This doesn't work at all. I don't think it makes sense to talk about stress regulating mitochondrial membrane polarisation. Reduced polarisation is a marker of stress not a response to it (although it may also occur for other reasons too).
Perhaps the confusion comes from me trying to make the definition fit the standard 'response to cellular stress pattern'. How about this:
definition: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) in response to the presence of one or more depolarised mitochondria."
Re the name - is it becuase 'reduced' sounds like a phenotype (as in 'reduced compared to wild-type')? Would depolarisation be better ? (It at least sounds like it is not comparative). I avoided using the term 'depolaristation' because these membranes are not completely depolarised, but I think the term is ambiguous enough that it could cover reduction in polarisation. So, happy to change to that if you think it is better.
The processes are out of my comfort zone but this seems suspiciously like experimental readout...it seems to be more about the assay than the process.
I think it would be useful to have Pascale comment as she has much experience distinguishing these for higher euks.
It is not. Please see
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028823/
&
http://emboj.embopress.org/cgi/pmidlookup?view=long&pmid=18200046
Note - we already have 'mitochondrial depolarisation' (GO_0051882).
If you are worried about mis-use of these terms to annotate from assays, perhaps we could put a comment on this an related terms warning about usage.
At editor's SF meeting -
Paola: Thou shalt not define continuants by their qualities. Better to talk of processes.
Agree that term should be "response to mitochondrial depolarisation"
Definition: definition: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) in response to the depolaristation of one or more mitochondria."
Added term with name and definition as in last comment.
Great, thanks David!
Paola
Thanks David!