Missing parent: mitochondrial chromosome packaging

[ValWood]

• GO term ID and label for which you request a new superclass

@hattrill do you think that
mitochondrial chromosome packaging
should be part_of

mitochondrial genome maintenance
The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.

currently it isn't.

Or should there be a grouping term mitochondrial genome organization?
Or should "mitochondrial genome maintenance" change to mitochondrial genome organization"
(maintenance is a bit odd, it sounds more like an outcome than a process here, these processes occur and the genome is 'maintained')

Notes:
Currently there are only 2 EXP annotations to "mitochondrial chromosome packaging"
one of these is SGD ABF1 and Candida GCF1 both of which are also annotated to mitochondrial genome maintenance

"mitochondrial chromosome packaging" is not even a child of mitochondrial organization...

• Reference(s), if appropriate
  PMID:nnnnnnn

[hattrill]

Looking at genes annotated directly with 'mitochondrial genome maintenance', looks like a very mixed bag - from DNA rep to metabolic pathway genes. This probably results from phenotype rather than gene function. 'mitochondrial DNA metabolic process' is part_of mitochondrial genome maintenance' which seems very broad.

I think that obsoleting 'mitochondrial genome maintenance' would be best and moving the annotations to the correct place.

As for 'mitochondrial genome organization' - seems like a better term. Might be nice to bring together 'mitochondrial chromosome packaging' and 'mitochondrial nucleoid organization' which seem to be divorced at the moment:

Would have thought that 'mitochondrial nucleoid organization' would be part_of 'mitochondrial chromosome packaging'?

[ValWood]

Would have thought that 'mitochondrial nucleoid organization' would be part_of 'mitochondrial chromosome packaging'?

I'm not sure.

A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the mitochondrial nucleoid. The mitochondrial nucleoid is the region of a mitochondrion to which the DNA is confined.

So it's the region, rather than the DNA. Although I am unsure how that would be used for a process. I never saw anything about as process to organize the nucleoid - it would be 'chromosome organization'
Note to self: 2 EXP annotations probably need inspecting

[ValWood]

1. This one could be GO:0000001
   Mrx6 regulates mitochondrial DNA copy number in Saccharomyces cerevisiae by engaging the evolutionarily conserved Lon protease Pim1.
   https://europepmc.org/article/MED/31532710

GO:0000001 (https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0000001/complete)
mitochondrion inheritance
Definition (GO:0000001 GONUTS page)
The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton. PMID:10873824 PMID:11389764

2. This one appears to be a phenotype:
   https://europepmc.org/article/MED/26666268
   CHCHD10 mutations promote loss of mitochondrial cristae junctions with impaired mitochondrial genome maintenance and inhibition of apoptosis.

CHCHD10 is a component of the mitochondrial contact site and cristae organizing system (MICOS) complex (Pfanner et al, 2014). The expression of CHCHD10 mutant alleles leads to MICOS complex disassembly, loss of mitochondrial cristae, and nucleoid disorganization leading to a defect in mtDNA repair after oxidative stress.

[ValWood]

PROPOSED ACTIONS

1. GO:0000002 mitochondrial genome maintenance
   The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.

Rename to "mitochondrial genome organization"
(which covers replication and segregation), annotations should be correct but this is less "phenotype-y)

2. Obsolete mitochondrial nucleoid organization (2 EXP) not a real 'GO process'

3. make mitochondrial chromosome packaging a descendant of the renamed GO:0000002 mitochondrial genome organization

CC @pgaudet @hattrill

[pgaudet]

It seems how you want to use "mitochondrial genome organization" does not fit the standard definition of other "organization" terms,

A process which results in the assembly, arrangement of constituent parts, or disassembly of a xx

So, I am not sure how "mitochondrial genome organization" covers replication and segregation; we don't have similar terms for other types of genomes. Would you change the definition?

[ValWood]

Yep they are differnet things.

Maybe we leave
"mitochondrial genome maintenance" for now
It's probably useful to have this grouping term, and we could decide later whether to refine it or make it 'do not annotate'
There are 170-175 EXP to "mitochondrial genome maintenance" (depending on where you look), 80 are direct.

For this ticket, can I place "mitochondrial chromosome packaging" under either "mitochondrial organization"

The definition of
GO:0007005 mitochondrion organization
is
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. PMID:9786946

So it probably fits best under here?

[ValWood]

I also don't know if we want to do anything about "nucleoid organization"
The nucleoid is a region rather than a structure.
Dynamic Structure: The nucleoid can change its shape and organization in response to cellular needs, such as replication and transcription.
This seems to be a consequence of other processes rather than an active process.
There are
GO:0090143 nucleoid organization (10 EXP)
GO:0090144 mitochondrial nucleoid organization (2 EXP)

[hattrill]

Looks like "nucleoid organization" could go - doesn't seem very well defined and has quite a shallow parentage.

Think putting "mitochondrial chromosome packaging" under "mitochondrial organization" seems like the best option.

[ValWood]

I'll open a new ticket for nucleoid. There are some other issues for this one

#29688

[ValWood]

I don't know how to fix this, it has an equivalence axiom

'chromosome organization'
and ('occurs in' some mitochondrion)

[ValWood]

Perhaps the solution is to create a term "mitochondrial chromosome organization" to fix the parentage?

[pgaudet]

To summarize: Is the proposed action to move "mitochondrial chromosome packaging" under either "mitochondrial organization"?

[ValWood]

option 1
mitochondrial chromosome packaging is_a mitochondrial organization

or option 2
mitochondrial chromosome packaging is_a GO_NEW mitochondrial chromosome organization is_a mitochondrial organization
(which matched better the nuclear terms)