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#9885 Merge MT-based flagellum into cilium?
closed-accepted
5
2014-03-27
2012-12-04
No
From Toby Gibson, EMBL Heidelberg:
"These organelles [flagellum/cilium] are homologous and the split into flagellum/cilium is arbitrary. Cells which have few but long cilia have them designated as flagella.
It follows that if the flagellum is an organelle, then so is the cilium. That doesn't seem to be the case however in gene ontology - see the attached figure.
Given the very high interest in ciliopathy diseases, it would be good if the cilia could be fixed in GO. They should be escalated to organellar status. And cilia and flagella should be treated equivalently in GO. "
[My response]
"So the reason for the current arrangement in GO is that 'flagellum' in GO includes both bacterial-type flagella and microtubule-based, eukaryotic flagella. Bacterial flagella do not have microtubules so are not types of cilia.
So I think the what I think you're suggesting is that microtubule-based flagellum (GO:0009434) is equivalent to cilium (GO:0005929)?
We could either merge the terms together, or make microtubule-based flagellum (GO:0009434) a sub-class of cilium (GO:0005929).
I'll make a tracker ticket for this to allow others to comment. In the meantime I'll go ahead and just make cilium is_a organelle."
[From Toby]
"So the bacterial flagella are not homologous with the eukaryotic ones. They should not use the same GO term.
I would personally be very happy with a merged term for the MT-based eukaryotic flagella/cilia. Then there should still be child terms for the categories that people operationally define such as the non-motile primary cilia. These are signalling antennae and their importance to the cell is quite different to motile flagella for example (although these are also sensory devices in flagellates)."
In fact 'cilium' is divided into:
cillium
---[i] motile cilium
---[i] primary cilium
------[i] motile primary cilium
------[i] nonmotile primary cilium
'motile cilium' are of 9 + 2 structure, and 'primary cilium' are of 9 + 0 structure (note: we need to improve the definitions of these terms to state this).
'motile primary cilium' is an unusual type of 9 + 0 cilium bearing dynein arms, which is found at the embryonic node during development (see PMID:17009929).
So the merge being proposed should actually be between microtubule-based
flagellum (GO:0009434) and motile cilium (GO:0031514).
If we went for the merge option, I think we'd also have to obsolete the generic 'flagellum' term, and just have 'bacterial-type flagellum' under 'cell projection'. 'microtubule-based
flagellum' would be a synonym for motile cilium (GO:0031514). 'sperm flagellum (GO:0036126)' would be an is_a motile cilium (GO:0031514).
Sent out obsoletion notice for flagellum (GO:0019861) and flagellum part (GO:0044460) for
15 Jan 2013.
Since cilia and flagella aren't used interchangeably in the literature, what's the harm in leaving flagellum terms as is?
Reply to Stan from Toby:
"An example of interchangeable use is IFT. The acronym for Intra-Flagellar Transport is standard usage for the extremely active biomedical ciliopathy field.
A second issue is that there is no clear way to distinguish between a cilium and a flagellum. Flagella are usually longer but where is the length cut-off above which a cilium must be a flagellum."
The next stage is the process terms that reference cilia/flagella. I wrote a big long post but it got deleted [sigh]
GO:0009296 flagellum assembly [lots of bacterial annotation]
GO:0043064 flagellum organization [1 direct bacterial annotation]
GO:0035084 flagellar axoneme assembly [no bacterial annotation]
GO:0007288 sperm axoneme assembly [no bacterial annotation]
I think GO:0009296 flagellum assembly will probably have to be obsoleted, and its annotations reannotated to cilium assembly ; GO:0042384 or bacterial flagellum assembly ; GONEW. We'll also need bacterial flagellum organization ; GONEW.
We might be able to keep the other 3 terms though.
If we keep GO:0043064 flagellum organization the name will be changed to GO:0043064 cilium organization.
We also have:
GO:0001539 ciliary or flagellar motility [many bacterial annotations]
GO:0003341 cilium movement [no bacterial annotation]
GO:0060285 ciliary cell motility [no bacterial annotation]
GO:0036142 flagellum movement [no annotations]
GO:0060286 flagellar cell motility [several bacterial annotations]
GO:0071945 regulation of flagellar cell motility by regulation of motor speed [2 annotations, both bacterial]
GO:0071974 microtubule-based flagellar cell motility [1 annotation, not bacterial]
Here's a summary of the proposed changes:
Keep
GO:0001539 ciliary or flagellar motility [many bacterial annotations]
GO:0003341 cilium movement [no bacterial annotation]
GO:0060285 ciliary cell motility [no bacterial annotation]
GO:0007288 sperm axoneme assembly [no bacterial annotation]
GO:0035083 cilium axoneme assembly
Name changes [also change parenatge]
GO:2000155 positive regulation of flagellar cell motility [no bacterial annotation] -> GO:2000155 positive regulation of ciliary cell motility
GO:0071945 regulation of flagellar cell motility by regulation of motor speed [2 annotations, both bacterial] -> GO:0071945 regulation of bacterial flagellum cell motility by regulation of motor speed
Merges
GO:0035084 flagellar axoneme assembly [no bacterial annotation] -> GO:0035083 cilium axoneme assembly
GO:0036142 flagellum movement [no annotations] -> GO:0003341 cilium movement
GO:0071974 microtubule-based flagellar cell motility [1 annotation, not bacterial] -> GO:0060285 ciliary cell motility
Obsoletions
GO:0060286 flagellar cell motility [several bacterial annotations]
GO:0009296 flagellum assembly [lots of bacterial annotation]
GO:0043064 flagellum organization [1 direct bacterial annotation]
GO:2000153 regulation of flagellar cell motility [2 bacterial annotations]
GO:2000154 negative regulation of flagellar cell motility [5 bacterial annotations]
New Terms
regulation of ciliary cell motility
negative regulation of ciliary cell motility
bacterial flagellum assembly
bacterial flagellum organization
bacterial flagellum cell motility
regulation of bacterial flagellum cell motility
This is the final, final set of changes!
Keep
GO:0001539 ciliary or flagellar motility [many bacterial annotations]
GO:0003341 cilium movement [no bacterial annotation]
GO:0060285 ciliary cell motility [no bacterial annotation]
GO:0007288 sperm axoneme assembly [no bacterial annotation]
GO:0035083 cilium axoneme assembly
Name changes [also change parenatge]
GO:2000155 positive regulation of flagellar cell motility [no bacterial annotation] -> GO:2000155 positive regulation of ciliary cell motility
GO:0071945 regulation of flagellar cell motility by regulation of motor speed [2 annotations, both bacterial] -> GO:0071945 regulation of bacterial flagellum cell motility by regulation of motor speed
GO:0035734 intraflagellar transport involved in flagellum organisation -> GO:0035734 intraflagellar transport involved in cilium organisation
GO:0045724 positive regulation of flagellum assembly [3 annotations, none bacterial] -> GO:0045724 positive regulation of cilium assembly
Merges
GO:0035084 flagellar axoneme assembly [no bacterial annotation] -> GO:0035083 cilium axoneme assembly
GO:0036142 flagellum movement [no annotations] -> GO:0003341 cilium movement
GO:0071974 microtubule-based flagellar cell motility [1 annotation, not bacterial] -> GO:0060285 ciliary cell motility
GO:1900172 regulation of flagellum movement [2 annotations, none bacterial] -> GO:0003352 regulation of cilium movement
GO:1900173 negative regulation of flagellum movement [0 annotations] -> GO:0003354 negative regulation of cilium movement
GO:1900174 positive regulation of flagellum movement [0 annotations] -> GO:0003353 positive regulation of cilium movement
GO:0036144 regulation of flagellum beat frequency [2 annotations, none bacterial] -> GO:0003356 regulation of cilium beat frequency
Obsoletions
GO:0060286 flagellar cell motility [several bacterial annotations]
GO:0009296 flagellum assembly [lots of bacterial annotation]
GO:0043064 flagellum organization [1 direct bacterial annotation]
GO:2000153 regulation of flagellar cell motility [2 bacterial annotations]
GO:2000154 negative regulation of flagellar cell motility [5 bacterial annotations]
GO:0030092 regulation of flagellum assembly [lots of bacterial annotation]
GO:0045718 negative regulation of flagellum assembly [1 bacterial annotation]
New Terms
regulation of ciliary cell motility
negative regulation of ciliary cell motility
bacterial-type flagellum assembly
bacterial-type flagellum organization
regulation of bacterial-type flagellum cell motility
cilium organization
regulation of cilium assembly
negative regulation of cilium assembly
Obsoletion notice went out 14 Feb 2013
Note to self: remember to do xps for new and existing terms.
process has_participant cc
Added:
ID: GO:1902019 Label: regulation of ciliary cell motility
ID: GO:1902020 Label: negative regulation of ciliary cell motility
ID: GO:1902021 Label: regulation of bacterial-type flagellar cell motility
Obsoleted:
GO:0060286 flagellar cell motility
GO:0009296 flagellum assembly
GO:0043064 flagellum organization
GO:2000153 regulation of flagellar cell motility
GO:2000154 negative regulation of flagellar cell motility
GO:0030092 regulation of flagellum assembly
GO:0045718 negative regulation of flagellum assembly
Okay, think this is now all done.