new component terms from MetaCyc

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Hi,

As part of the MetaCyc project, we recently developed a cell component ontology. The component terms in the attached file are not in GO and you may find them useful to make the GO component terms more complete.

Please let me know if you have any questions regarding the file.

Best Regards,

Peifen

Peifen Zhang TAIR

Reported by: peifenz

Original Ticket: "geneontology/ontology-requests/2831":https://sourceforge.net/p/geneontology/ontology-requests/2831

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new terms

Original comment by: peifenz

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Original comment by: mah11

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Instead of space, why not create a more specific, biologically relevent term, "membrane-enclosed lumen" defined as follows.

The enclosed volume within a sealed membrane or between two sealed membranes.

"membrane-enclosed lumen" could then be a direct is-s of cellular component, and have all the children suggested for "space."

(Note that the qualifier "membrane-enclosed" is needed to distinguish this type of lumen from enclosed body spaces such as the lumen of an artery or the instestinal lumen.)

-- Alex

Original comment by: addiehl

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There's 'organelle lumen' (GO:0043233) ... would that be the same, or a child? The definition sounds similar: 'The volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear membrane lumen.'

Original comment by: mah11

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"Organelle lumen" does seems like an appropriate parent to all the suggested children of "space," given the GO definition of organelle. I suggest we use that as the parent term instead of "space."

-- Alex

Original comment by: addiehl

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Hi,

First of all, the suggested terms should be children of organelles(eg chloroplast) in addition to the suggested parentage such as plasma membrane etc.

1. term: chloroplast thylakoid membrane definition: The pigmented membrane of any chlosoplast thylakoid.

We have a term thylakoid membrane (sensu Viridiplantae) The pigmented membrane of a thylakoid. As in, but not restricted to, green plants and algae (Viridiplantae, ncbi_taxonomy_id:33090).

Are they not the same?

2. We don't need the plasma membrane(sensu xxx) terms in GO. We are not distinguishing the membranes based on what they are surrounded by unless it breaks the TP rule.

3. chloroplast thylakoid lumen definition: The space enclosed by the membrane of any chloroplast thylakoid.

We have thylakoid lumen (sensu Viridiplantae) A cavity enclosed within the thylakoid membrane. As in, but not restricted to, green plants and algae (Viridiplantae, ncbi_taxonomy_id:33090).

These are the same terms again.

4. I vote to keep the 'nuclear membrane' term in GO and use envelope as a synonym as it has been. There is no difference in definition of the existing 'nuclear membrane' term and the suggested 'nuclear envelope' term.

5. term: chloroplast stacked thylakoid definition: A set of flattened disc-like sacs formed by the thylakoid membrane. They are interconnected and often arranged in stacks, and referred as grana.

GO has

granal stacked thylakoid Appressed thylakoid membranes that are part of a granum (stacked regions). A characteristic of these appressed regions is the preferential localization of photosystem II.

thylakoid (sensu Viridiplantae) Sac-like membranous structures (cisternae) in a chloroplast combined into stacks (grana) and present singly in the stroma (stroma thylakoids or frets) as interconnections between grana. As in, but not restricted to, green plants and algae (Viridiplantae, ncbi_taxonomy_id:33090).

I agree with Alex's comment. Term 'space' is not strictly tied to cellular components. Space could be any space....

Cheers, Suparna

Original comment by: smundodi

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"organelle lumen" sounds to me a child term of space. It does not accommodate cytosol, periplasmic space, extracellular space.

Peifen

Original comment by: peifenz

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Regarding Suparna's comment on using the name 'nuclear membrane' VS 'nuclear envelope', I agree their definition is about the same. But the GO definition of 'nuclear membrane' is quite different from the definitions of many other GO membrane terms, such as 'endosome membrane'. The 'nuclear membrane' is defined as two membranes plus the intermembrane space. It is not really a membrane term per sa. Why not make the term intuitive and distinguishable for users by using 'nuclear envelope'. You would want to have people rely on an intuitive name as much as possible, rather than letting them check definitions every time. Especially, you are already using the term 'chloroplast envelope' to highlight the fact that it is a double-membrane structure. Why not use the envelope terms consistent through out GO?

Peifen

Original comment by: peifenz

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The problem with 'nuclear membrane' is that biologists have used it inconsistently -- because 'nuclear membrane' is often used with the meaning 'nuclear envelope', it's not necessarily intuitive to build a distinction into GO. We therefore have to decide whether the consistency we gain is worth doing something a bit different from what's used in the literature, which is why I've put it to the mailing list.

m

Original comment by: mah11

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I've added some of the non-controversial terms:

chromoplast envelope GO:0031898 chromoplast inner membrane GO:0031899 chromoplast outer membrane GO:0031900 early endosome membrane GO:0031901 late endosome membrane GO:0031902 microbody membrane GO:0031903 endosome lumen GO:0031904 early endosome lumen GO:0031905 late endosome lumen GO:0031906 microbody lumen GO:0031907 glyoxysomal lumen GO:0031908 peroxisomal lumen GO:0031909

Original comment by: mah11

[gocentral]

• summary: new terms --> new component terms from MetaCyc

Original comment by: jl242

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I do agree that we have to sort out this envelope v/s membrane distinction though, and make ourselves internally consistent. At the moment the double layered structure of plastids is called 'plastid membrane' and has the part_of children 'inner plastid membrane' and 'outer plastid membrane' - this is very odd. Meanwhile, chloroplasts, which are plastids, have a 'chloroplast envelope' resulting from the changes below. This has lead to some incorrect and missing relationships (I spotted them from an OBOL report on weird part_ofs in CC).

I really don't like using nuclear membrane in place of nuclear envelope - aren't we just adding to the ambiguity by continuing to use the term incorrectly in GO? Did you get any response from the list to your email Midori?

So - does anyone mind if fix the terms that say 'membrane' for a double membrane structure to say 'envelope'? I'll leave the nuclear membrane for now.

Original comment by: jl242

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> aren't we just adding to the ambiguity by > continuing to use the term incorrectly in GO?

what we're doing is following a common usage in the literature ... whether that's 'incorrect' or not depends on your definition of 'incorrect'. At present GO is neither more nor less ambiguous than the literature; we have the option of becoming less ambiguous, at the price of being a little bit less similar to the literature. Deviating from usages common among biologists tends to rile some people, so that's why I've been hoping for more input than we've had so far. (For myself, I'm quite willing to go the less ambiguous route, but I really don't want it to take anyone by surprise.)

> Did you get any response from the list to your email, Midori?

ha! (i.e. not a peep on the list; a couple of the comments below came after, and probably as a result of, that email, but they mostly dealt with the organelle lumen terms)

> So - does anyone mind if fix the terms that say 'membrane' > for a double membrane structure to say 'envelope'?

I'd prefer to wait for a real response from the list, but that may be unrealistic. (sigh)

m

Original comment by: mah11

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• assigned_to: nobody --> gomidori

Original comment by: mah11

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I've now done most of the outstanding work on this item. The only thing remaining now is:

term: cell envelope (sensu Bacteria) term: cell envelope (sensu Gram-negative Bacteria) term: cell envelope (sensu Gram-positive Bacteria)

The existing prokaryote cell envelope terms have been vetted by Michelle Gwinn, so we will only change them with her approval. I've emailed to ask her to look at these suggestions.

We have used Alex's suggestion, 'membrane-enclosed lumen', instead of 'space'.

As Suparna has noted, at present GO does not distinguish cellular components based on what they are surrounded by, so I have not added the children of plasma membrane:

term: plasma membrane (sensu Bacteria) term: plasma membrane (sensu Gram-negative Bacteria) term: plasma membrane (sensu Gram-positive Bacteria) term: plasma membrane (sensu Fungi)
 term: plasma membrane (sensu Animalia) term: plasma membrane (sensu Magnoliophyta)

We may decide to add surrounded-by distinctions at a later date; if so, we can add these terms then.

What is done:

renamed GO:0005635 to 'nuclear envelope' renamed GO:0005641 to 'nuclear envelope lumen' (keeping old wording as synonym) renamed GO:0005740 to 'mitochondrial envelope'

added GO:0031965 nuclear membrane GO:0031966 mitochondrial membrane (defined as either of the lipid bilayers, but excluding the lumen)

removed synonym from GO:0005635

moved terms so that all of the above have correct parents nuclear envelope is_a organelle envelope, etc.

also added GO:0031967 organelle envelope GO:0031968 organelle outer membrane GO:0031969 chloroplast membrane GO:0031970 organelle intermembrane space GO:0031971 mitochondrial envelope lumen GO:0031972 chloroplast intermembrane space GO:0031973 chromoplast intermembrane space GO:0031974 membrane-enclosed lumen GO:0031975 envelope GO:0031976 plastid thylakoid GO:0031977 thylakoid lumen GO:0031978 plastid thylakoid lumen GO:0031979 thylakoid lumen (sensu Cyanobacteria) GO:0031980 mitochondrial lumen GO:0031981 nuclear lumen GO:0031982 vesicle GO:0031983 vesicle lumen GO:0031984 organelle subcompartment GO:0031985 Golgi cisterna GO:0031986 proteinoplast

also renamed GO:0019866 to 'organelle inner membrane' (consistent with def and children)

corrected relationships for existing plastid membrane (9527, 9528, 42170) and plastid envelope (9526) terms

removed relationship 5639 is_a 19866

added synonyms chloroplast thylakoid 9534 chloroplast thylakoid membrane 9535 chloroplast stacked thylakoid 9515

m

Original comment by: mah11

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From Michelle Gwinn on cell envelope terms:

---

Hi Midori,

I can live with expanding the definition of cell envelope to include the cytoplasmic membrane, but otherwise I like the GO definition better and in fact it should actually be expanded. The proposed definition below leaves out a key part of the envelope which is the periplasmic space.
An important part of the current GO def is that it says "everything" outside the cell membrane, rather than restricting the def to just a few named things. There are layers of LPS, protein, and phospholipids that are part of the Gram negative envelope. In fact the term "cell envelope" in my experience is only used with Gram negatives, and that is what my textbook says. But I have seen instances of its use with positives, even though I don't think its technically correct. So, I'm not sure there should really be a Gram positive envelope term, but I'm not sure enough to oppose it.

How about this:

cell envelope Everything external to and including the cytoplasmic membrane of bacteria, including, but not limited to, the periplasmic space, cell wall, and outer membrane if present.

cell envelope Gram negative Everything external to and including the cytoplasmic membrane of Gram negative bacteria, including, but not limited to, the periplasmic space, cell wall, and outer membrane.

cell envelope Gram positive Everything external to and including the cytoplasmic membrane of Gram positive bacteria, including the cell wall.

Michelle

It seems that if it's true that Gram-positive bugs don't have structures that would be called 'cell envelopes', the existing GO terms are sufficient.

m

Original comment by: mah11

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Based on Michelle's comments, I'll leave the cell envelope term unchanged for the time being. If a need for a Gram-positive term arises in the future, we will add it then.

m

Original comment by: mah11

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• milestone: --> TAIR
• status: open --> closed-accepted

Original comment by: mah11