checkup on the "cilium" terms

[gocentral]

I found the terms under "cilium" a bit confusing and perhaps at odds with current literature in how they use "primary", "secondary", "motile", and "nonmotile". I suggest a review of these terms to see if clarity can be achieved. Here is an email thread I originally posted on the GO list. Kimberly graciously stepped forward to help have a look at these terms since they originated from her several years ago.

Hi Doug,

I had worked on adding these terms to GO about five or six years ago, so it might well be worth it to see if they still reflect the current knowledge or if we need to update the defs, add synonyms, new terms, etc.

If you have suggestions, please forward them along. I'll try to take a look at some more recent literature to see what I can find, too.

Thanks, --Kimberly

I'm needing to use the GO terms relating to 'cilium' but I'm having a hard time disambiguating them and figuring out which one(s) to use. Most papers I see seem to refer to 2 types of cilia.

1) motile (primary) cilia with a 9+2 organization 2) nonmotile (secondary) cilia with a 9+0 organization

Go seems to have a third choice for a "nonmotile primary cilium" having a 9+0 organization.

The zebrafish literature indicates that Kupffer's vesicle and the pronephric duct have primary and secondary cilia..but I can't disambiguate these in the GO. The papers I've seen seem to use "primary" and "secondary' as synonymous with "nonmotile" and "motile" respectively, while the GO seems to use "primary" and "secondary" to mean 9+0 or 9+2 structure and "motile" and "nonmotile" to mean motile and nonmotile.

Can anyone clarify?

-Doug

Reported by: doughowe

Original Ticket: geneontology/ontology-requests/7934

[gocentral]

Hi Doug,

I'm reading PMID:19345185 and looking at the chart in Figure 1.

Trying to figure out a way to represent this better; looks like rabbits even have a 9+4 configuration!

--K.

Original comment by: vanaukenk

[gocentral]

No wonder I was confused. Looks like a Cartesian product...both motile and primary cilia can be 9+2 or 9+0...and then there is 9+4 and perhaps others yet to be discovered. Seems like we could simplify the GO to just capture the two major classes as 'primary cilium' and 'motile cilium' (I think we should at least do this). We could then, for the sake of completeness, expand below that as needed to represent specific cases of 'motile' or 'primary' or configurations. With this structure it is easy to expand for any new types that may come up and curators can annotate to whatever level of detail they feel confident.

What do you think of this?

cilium ....[i] primary cilium .......[i] primary 9+2 cilium .......[i] primary 9+0 cilium ....[i] motile cilium ......[i] motile 9+2 cilium ......[i] motile 9+0 cilium ...[i] 9+2 cilium ......[i] primary 9+2 cilium ......[i] motile 9+2 cilium ...[i] 9+0 cilium ......[i] primary 9+0 cilium ......[i] motile 9+0 cilium ...[i] 9+4 cilium

Original comment by: doughowe

[gocentral]

Hi Doug,

I like the idea of making specific terms for each of the cilium configurations, i.e. 9+0, 9+2, or 9+4 (if you're a rabbit). I think it's more precise.

However, I wonder if we should use non-motile cilium and motile cilium, as opposed to primary and motile? Here is a paragraph from PMID:19439065 that seems to support this type of distinction:

"The traditional classification of cilia into two main classes, motile 9+2 and non-motile 9+0, is insufficient to reflect the complexity of all cilia types. The most recent studies indicate that cilia can be divided into at least four main cilia types: motile 9+2, motile 9+0, non-motile 9+2 and non-motile 9+0. In the 9+2 configuration the axoneme contains a central microtubule pair surrounded by the nine microtubule doublets, which is missing in the 9+0 configuration. Moreover, motile cilia contain inner and outer dynein arms, radial spokes and nexin links (reviewed in [1]). Inner and outer dynein arms on the doublets mediate axoneme motility. The radial spokes play an essential role in the control of dynein arm activity by relaying signals from the central pair of microtubules to the arms. Nexin links are the connecting links between microtubules in cilia and flagella. Radial cuts of 9+0 and 9+2 axonemal structures of non-motile and motile cilia, respectively, are illustrated in Figure 1A and 1B. Respiratory and ependymal cilia are motile 9+2 with a back-and-forth motion. In the murine embryonic node, primary cilia are an admixture of 9+2 and 9+0 cilia [2]. The specific feature of the unique 9+0 motile cilium is the rotational movement generating an anti-clockwise flow of extra-embryonic fluid in the nodal area [3]. Thus, the central microtubule pair seems to be required for back-and-forth movement while its absence produces a rotational movement. Non-motile 9+2 cilia are present on specialized olfactory neurons [4]. Renal monocilia, photoreceptor-connecting cilia and cilia of pancreatic islets are non-motile 9+0 cilia [5-7]. Finally, among the different cilia types, 9+4 cilia have been identified on the notochordal plate of the rabbit embryo [8]."

We could add synonyms to the nonmotile cilium terms to reflect that these are often referred to as primary cilium in the literature.

Does that still fit with what you see in zebrafish?

Thanks, --K. .

Original comment by: vanaukenk

[gocentral]

Yep..I think we should settle on "primary" and "secondary" OR "sensory' and "motile" an use synonyms liberally. So a new structure might look like this (with "primary" being used a synonymous with "sensory"):

cilium ....[i] sensory cilium .......[i] sensory 9+2 cilium .......[i] sensory 9+0 cilium ....[i] motile cilium ......[i] motile 9+2 cilium ......[i] motile 9+0 cilium ...[i] 9+2 cilium ......[i] sensory 9+2 cilium ......[i] motile 9+2 cilium ...[i] 9+0 cilium ......[i] sensory 9+0 cilium ......[i] motile 9+0 cilium ...[i] 9+4 cilium

I'm not sure if the rabbit 9+4 case is sensory or motile, so I left it out as just a 9+4 stub. Can be expanded if more info comes to light.

Original comment by: doughowe

[gocentral]

Hi--

It looks like motile cilia can also have sensory functions (see below), so I think I still prefer motile and nonmotile as the primary distinction with, as you say, liberal addition of synonyms.

What do you think?

From PubMed (PMID:20144998)

Sensory reception is an attribute of both primary cilia and motile cilia.

Bloodgood RA.

Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22908-0732, USA. rab4m@virginia.edu Abstract

A recent cluster of papers has shown that motile cilia in the respiratory and reproductive tracts of humans and other mammals can exhibit sensory functions, a function previously attributed primarily to non-motile primary cilia. This leads to a new paradigm that all cilia and flagella (both motile and primary) can mediate sensory functions. However, examination of the literature shows that evidence of sensory functions of motile cilia and flagella is widespread in studies of invertebrates, and extends as back as far as 1899. In this Opinion article, I review the recent and historical findings that motile cilia have a variety of sensory functions, and discuss how this concept has in fact been evolving for the past century.

PMID: 20144998

Original comment by: vanaukenk

[gocentral]

Oh good grief...right....I forgot about that little detail. I'm a little leary of "nonmotile" because it is a class by exclusion...meaning all cilia but the motile ones. Now, maybe there is only one thing in this class...but it opens us up to the possibility of inclusion of more than one type of cilium which is not motile. If we went with "motile" and "primary" this avoids the lack of positivity inherent in "nonmotile". Of course....if the research community have gravitated primarily to "motile" and "nonmoile" we can go that way. If they have gravitated to "motile' and "primary" I might prefer that route though...

Original comment by: doughowe

[gocentral]

Searching pubmed I find the following counts when searching these strings:

"secondary cilia" 7 "motile cilia" 178 "nonmotile cilia" 11 "non-motile cilia" 7 "primary cilia" 555 "sensory cilia" 169

So, it looks like between "primary" and ["nonmotile"|"non-motile"], "primary" is a clear winner.

I feel like we should go with "primary cilium" and "motile cilium".

I don't want to add a third axis of differentiation by adding terms like "motile cilium with sensory functions", "motile 9+2 cilium with sensory functions", "motile 9+2 cilium without sensory functions"..etc....just say no to those terms...

Original comment by: doughowe

[gocentral]

Hi--

Yes, primary and motile are the terms I've seen most often in the literature.

How should we define primary cilium in GO, then? I think before we'd defined it as generally a 9+0 cilium, but that won't work any more, right?

Original comment by: vanaukenk

[gocentral]

I guess we need to figure out how a researcher decides which it is. Maybe that distinction is becoming blurred and it isn't a real distinction at all....even if researchers use those names. It's kind of like calling a neuron "cholinergic" because of one of the many things it releases....

I guess a "motile" cilium is one which lacks a sensory role (that we know about) and a "primary" cilium is one which is purely sensory (as far as we know)...and the ones that are both motile and sensory are a third catagory?

Alternatively...it is starting to sound to me like "motile" and "primary" are not real distinct types anyway..so we could drop them from the ontology as an axis of differentiation...? Seems kind of radical...but might be better ontologically..?

cilium .....9+2 cilium .....9+0 cilium .....9+4 cilium

As far as I can tell this is the most conservative and 100% correct representation...but it will be hard for users and curators who are looking for "motile cilium"....which they will look for...

Original comment by: doughowe

[gocentral]

Hi--

I think I'm going to need to think about this some more. I'm trying to come up with definitions for primary vs motile cilia and then see what exceptions might cause the definitions to be incorrect.

I'll try to post them tomorrow.

Thanks, --K.

Original comment by: vanaukenk

[gocentral]

Sorry for going 'round and 'round on this...I've come full circle back to this structure:

cilium ....[i] primary cilium .......[i] primary 9+2 cilium .......[i] primary 9+0 cilium ....[i] motile cilium ......[i] motile 9+2 cilium ......[i] motile 9+0 cilium ...[i] 9+2 cilium ......[i] primary 9+2 cilium ......[i] motile 9+2 cilium ...[i] 9+0 cilium ......[i] primary 9+0 cilium ......[i] motile 9+0 cilium ...[i] 9+4 cilium

Seems from PMID:20144998 that the ability to possess a sensory role is just an attribute of a motile or a primary cilium. It either does or does not trasmit sensory information. I think as long as we do not bring that into the definitions for these, then they should be fine.

Like you said, we just need to figure out how to define primary and motile..then we are golden I think.. A primary cilium is ? A motile cilium is ?

Original comment by: doughowe

[gocentral]

Seems to me like the true distinguishing feature of a "primary" from a "motile" is that primary cilia occur in only one or two per cell, while motile cilia occur in bundles of many per cell. Either can have sensory functions and either can be 9+0 or 9+2 or some other configuration.

http://www1.bio.ku.dk/english/research/cu/cilia/

This should be an integral part of the definitions I think.

Original comment by: doughowe

[gocentral]

Hi Doug,

Yes, I think we're on the right track. I was just making a list of what are the different characteristics of cilium:

1) what cell types they're on 2) how many per cell 3) the MT arrangement 4) motile or nonmotile 5) if motile, what type (beat or whirl) 6) presence or absence of dynein 7) function - sensory, fluid movement

So, maybe we can construct new definitions for the existing GO terms to broaden them to include more recent information, such as the variety of MT arrangements that have been observed. I think the basic structure we have in GO right now is okay, but the definitions are too limiting.

--K.

Original comment by: vanaukenk

[gocentral]

Here are some revised definitions. Do these work for your annotations?

nonmotile primary cilium

An immotile primary cilium that may be missing the central pair of microtubules, or the central pair of microtubules and outer dynein arms. Some primary cilia also have altered arrangements of outer microtubules (fewer than nine and/or not always present as doublets). Nonmotile primary cilia generally occur in one or two per cell, are found on nearly all cell types, and typically function as sensory organelles that concentrate and organize sensory signaling molecules. [source:]

motile primary cilium Synonym: nodal cilium

A specialized primary cilium that contains a 9 + 0 arrangement of microtubules, radial spokes, and a dynein apparatus, but no inner doublet microtubules. Motile primary cilia occur in one per cell, display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface and can function in determining left-right asymmetry during embryonic development. [source:]

motile cilium

A cilium that typically consists of a 9 + 2 arrangement of microtubules, radial spokes, and a dynein apparatus. Motile cilia occur in bundles of many per cell on epithelial cells that line the lumenal ducts of various tissues. Motile cilia beat with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia can also function in sensory transduction. [source:]

Source/References: PMID: 17009929, PMID: 20144998, http://www1.bio.ku.dk/english/research/cu/cilia/

Original comment by: vanaukenk

[gocentral]

Are there differences between fish and mammalian nodal cilia? Do we need to further revise the definition for motile primary cilium to make sure we can include both types?

Original comment by: vanaukenk

[gocentral]

Hi Kimberly, Would these be organized like this then?

cilium .....primary cilium .......nonmotile primary cilium .......motile primary cilium ....motile cilium

The paper I'm working on simply discusses "primary cilia"...so I can't tell if it is motile or nonmotile in this case. it would be good to have the structure shown above in this case?

Though confusing due to the fact that "motile primary cilium" is not a type of "motile cilium" (maybe should put that fact in the comment so no one adds that apparently obvious but incorrect relationship later), this does represent the different types as I understand them currently.

Original comment by: doughowe

[gocentral]

I think we need def. revision for motile primary cilium. From a zebrafish paper:

From ZDB-PUB-050328-4: Results "Apical cilia are present in KV, in the central canal of the spinal cord, and in the pronephric ducts To survey zebrafish larvae for the presence of ciliated cells during organogenesis, we performed immunocytochemistry using an anti-acetylated tubulin antibody. Immunostaining confirmed an earlier report that apical cilia are present in cells lining KV at the 8-somite stage (Fig. 1A,D) (Essner et al., 2002). Also, ependymal cells along the central canal bore apical cilia at 24hpf (Fig. 1B,E), as did pronephric duct cells at 48hpf (Fig. 1C,F). KV cilia and pronephric duct cilia showed an ultrastructure consisting of nine peripheral microtubules and a central pair (9+2 pattern; Fig. 1G,I), whereas a 9+0 formation was present in ependymal cell cilia along the central canal of the spinal cord (Fig. 1H). Outer dynein arms were present in cilia of all three organs (arrows). All kidney cilia examined were 9+2; no 9+0 cilia were found in the zebrafish pronephros."

Original comment by: doughowe

[gocentral]

Hi,

Yes, I think that the ontology structure below would work and I agree that we should add a comment, probably to both motile cilia and motile primary cilia, to make sure that these two terms don't one day end up with a parent-child relationship.

cilium .....primary cilium .......nonmotile primary cilium .......motile primary cilium ....motile cilium

For revising motile primary cilium, how about the following (and adding yet another reference, PMID: 15716348):

motile primary cilium Synonym: nodal cilium

A specialized primary cilium that can contain a 9 + 0 or 9+2 arrangement of microtubules, radial spokes, and a dynein apparatus. Motile primary cilia occur in one per cell, display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface and can function in determining left-right asymmetry during embryonic development. [source:]

Original comment by: vanaukenk

[gocentral]

Getting closer...

Because of stuff like this:

Am J Anat. 1985 Dec;174(4):437-53. Observations on the solitary cilium of rabbit oviductal epithelium: its motility and ultrastructure.

Odor DL, Blandau RJ. Abstract

Solitary cilia have been observed on rabbit oviductal epithelial cells. In tissue cultures of fimbrial epithelium of 3- and 4-day-old animals observed by phase microscopy, most of these single cilia exhibited a vortical or funnel-type movement while others had the usual to-and-fro motility. Primary cilia are usually considered immotile. ...[CROP].........Cross sections of the single cilia showed patterns of microtubules different from the usual 9 + 2 axonemal complexes of normal cilia and included 9 + 0, 10 + 2 singlets, 7 + 2 doublets, and 8 + 1 doublet and 2 singlets; one did have the usual 9 + 2 arrangement.

PMID: 3909797 [PubMed - indexed for MEDLINE]

We should probably stick to a simpler GO ontology like this: cilium ...primary cilium ......nonmotile primary cilium ......motile primary cilium ...motile cilium

Then just soften the defs to allow for various microtubule structures in each case. As far as I can tell, you can have just about any microtubule structure and be motile or nonmotile...the two are not strongly correlated. Maybe the defs shouldn't even say anything about the microtubule structures?

Could be something like this:

motile primary cilium: "A specialized primary cilium that has radial spokes and a dynein apparatus. Motile primary cilia generally occur one per cell, display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface and can function in determining left-right asymmetry during embryonic development. [source:]

?

If we go that way we should remove references to microtubule structure in the other defs as well...

Original comment by: doughowe

[gocentral]

I have been following this discussion with interest ... nay, fascination. I don't have any cilium-specific knowledge to offer, but I'm very happy to do the editing when you have the structure, defs, etc. sorted out.

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Hi--

Here are some suggested new term names, definitions, and comments for the cilium branch. For each of the definitions, I would at least cite PMID:17009929 and PMID:20144998 as reference sources and would be happy to include more, if needed.

Please tweak as needed

cilium GO:0005929 -primary cilium GO:NEW --motile primary cilium GO:00031512 --nonmotile primary cilium GO:0031513 -motile cilium GO:0031514

Original definition of parent term cilium would remain the same.

primary cilium GO:NEW A cilium found on many different cell types that is typically present in a single copy per cell. A primary cilium may have a variable array of axonemal microtubules and may or may not contain molecular motors.

nonmotile primary cilium GO:0031513 An immotile primary cilium found on many different cell types that is typically present in one copy per cell. A nonmotile primary cilium may have a variable array of axonemal microtubules, but does not contain molecular motors. Nonmotile primary cilia typically function as sensory organelles that concentrate and organize sensory signaling molecules.

motile primary cilium GO:0031512 Related synonym: nodal cilium A specialized embryonic primary cilium that contains a variable arrangement of axonemal microtubules and also contains molecular motors. Motile primary cilia display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization Comment. Motile primary cilia are distinct from motile cilia (GO:0031514) that are typically present on epithelial cells in multiple copies and move in a whip-like, as opposed to rotational, manner.

motile cilia GO:0031514 (note the removal of the term secondary) A cilium typically found in multiple copies on epithelial cells that line the lumenal ducts of various tissues. Motile cilia may have a variable arrangement of axonemal microtubules, contain molecular motors, and beat with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia may also function as sensory organelles. Comment: Motile cilia are distinct from motile primary cilia (GO:0031512) that are typically present during embryogenesis in a single copy per cell, affect asymmetric body plan organization, and move in a rotational manner, as opposed to a whip-like, manner.

--K.

Original comment by: vanaukenk

[gocentral]

This looks good; thanks for doing all the legwork! Just a couple small things:

- Would the children of nonmotile primary cilium stay the same?

- Both the new and existing defs seem to bounce between "immotile" and "nonmotile". Any reason not to use "nonmotile" everywhere? And should we add synonyms for the terms with "nonmotile" in the names?

Anyway, let me know when you both agree it's ready to go, and I'll edit.

m

Original comment by: mah11

[gocentral]

I've made a few small rearrangements to the defs. Otherwise this seems to reflect reality pretty well..

primary cilium GO:NEW A cilium found on many different cell types that is typically present in a single copy per cell. A primary cilium may have a variable array of axonemal microtubules and may or may not contain molecular motors.

nonmotile primary cilium GO:0031513 A primary cilium which contains a variable array of axonemal microtubules but does not contain molecular motors. Nonmotile primary cilia are found on many different cell types and function as sensory organelles that concentrate and organize sensory signaling molecules. Exact Syn: immotile cilium Exact Syn: sensory cilium

motile primary cilium GO:0031512 Related synonym: nodal cilium A primary cilium which may contains a variable array of axonemal microtubules and also contains molecular motors. Motile primary cilia display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Comment. Motile primary cilia are distinct from motile cilia (GO:0031514) that are typically present on epithelial cells in multiple copies and move in a whip-like, as opposed to rotational, manner.

motile cilium GO:0031514 (note the removal of the term secondary) A cilium which has a variable arrangement of axonemal microtubules, contains molecular motors, and beats with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia are typically found in multiple copies on epithelial cells that line the lumenal ducts of various tissues. with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia may also function as sensory organelles. Comment: Motile cilia are distinct from motile primary cilia (GO:0031512) that are typically present during embryogenesis in a single copy per cell, affect asymmetric body plan organization, and move in a rotational manner, as opposed to a whip-like, manner.

Original comment by: doughowe

[gocentral]

For you copy/paste editors out there...beware I accidentally left an extra "s" in the def of "motile primary cilium".

Def should start "A primary cilium which may contain...."

Original comment by: doughowe

[gocentral]

Hi--

I just double-checked the children of nonmotile primary cilium, photoreceptor outer segment and kinocilium, and their placement in the graph is still okay.

With regard to the use of immotile and nonmotile, I've seen both used in the literature. I think we could stick with the use of nonmotile in the term name and definitions, but, as Doug has done, add immotile to the synonym list.

e.g. immotile cilium immotile primary cilium sensory cilium

Midori, does GO have a standard policy about including plurals as synonyms? i.e., should we also include nonmotile primary cilia and immotile primary cilia, etc. as synonyms?

Original comment by: vanaukenk

[gocentral]

Great! I should be able to do the editing for this some time this week. I'll include all the suggested synonyms -- there isn't exactly a hard-and-fast policy on plural synonyms, but there's nothing forbidding them. There is a general tendency to err on the side of including synonyms, especially in cases like this where the synonym phrasing is so commonly used.

Original comment by: mah11

[gocentral]

Okay, great. Thank Midori. Let us know if any questions come up.

Original comment by: vanaukenk

[gocentral]

OK, I think I've implemented everything. Of course, do holler if I missed or botched anything. It's been a really interesting discussion.

m

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• status: open --> closed-fixed

Original comment by: mah11