Chromatophore terms (Paulinella)

There are a number of new Subcellular Location terms in UniProt that I am trying to map to GO.

The terms are Chromatophore, Chromatophore inner membrane, C. intermembrane space, C. membrane, C. outer membrane, C. stroma, C. thylakoid, C. thylakoid lumen and C. thylakoid membrane.

In the literature there are several types of chromatophore, i.e. pigment-containing cells (Amphibians, reptiles etc.), coloured membrane-associated vesicles (Photosynthetic bacteria) and photosynthetic plastid-like organelles (the amoeboid Paulinella). GO has the term chromatophore in the sense of photosynthetic bacteria which corresponds to the Subcellular Location term 'cellular chromatophore', however the new chromatophore terms have been made specifically for the plastid-like organelles found in Paulinella. I have communicated with the subcell curators (see email below) who have had problems with the naming of these terms since chromatophore has several different meanings.

If I were to request these terms in GO, are there any suggestions as to what we could name them to distinguish them from the bacterial chromatophore?

Also, the subcell curator seems to think that the GO definition of chromatophore shouldn't include cyanobacteria as the structures found in these are actually thylakoids. I have found this very long link to a book which says a similar thing; http://books.google.co.uk/books?id=xgMahO1BXrQC&pg=PA292&lpg=PA292&dq=cyanobacteria+thylakoid+chromatophore&source=web&ots=m5ahhZ5Prm&sig=XE-oEV4f56urmKPW0FFWdTDkyFY&hl=en&sa=X&oi=book\_result&resnum=1&ct=result but the definition in Merriam-Webster includes the cyanobacteria.

Any comments welcome! Rachael.

> Dear Rachael, > > This is a bit of a rat's nest I'm afraid. > > Paulinella chromatophora is a eukaryote, and has an oxygenic, photosynthetic intracellular organelle that is (unfortunately) called a chromatophore. Chromatophore is used in several other organisms than Paulinella, including not just the purple photosynthetic bacteria but also cells in reptiles, fish etc, responsible for skin and eye colour. I think one can also use the term for certain types of cells in humans (look at wikipedia for example). This is very unfortunate, but the term is so old that I do not think anyone would use another term for Paulinella chromatophora. One of the plant annotators and I went around the question several times and could never find another solution we liked... > > The membranes in the anoxygenic purple photosynthetic bacteria come under the heading "Cellular chromatophore" (SL0042), which we have tried to make distinct from Plastid, chromatophore. Thus there is already a separate definition for the bacteria. If I tried to add the bacteria to the plastid it would not make biological sense, and would make a mess of the hierarchy of our subcellular location terms. Incidentally I do not think your chromatophore definition is quite correct; as far as I know chromatophore is not used in cyanobacteria which are oxygenic. The photosynthetic membranes in cyanobacteria are called thylakoids, as they are in photosynthetic eukaryotes. > > As for the internal compartments the term thylakoid has been used once in the literature. Not reading German I have simply relied on the translation of the author's abstract (PubMed 4208322, Protoplasma 80:69-89(1974), I'll paste the translation below). Seeing as we are annotating orthologues of well characterized proteins I need a name for the compartments they are going to be found in and I have assumed, based on the abstract below as well as other work, that they will look a lot like other organelles. In short seeing as the term thylakoid has been used I decided envelope, stroma and lumen would also make sense. If the people who work on Paulinella change the terms I will of course follow course. > >> Summary The ultrastructure of the sausage-shaped cyanelles and the ultrastructure and formation of the thecal scales of/Paulinella chromatophora/ were investigated. The cyanelles have a 6–13 nm thick wall. They are lying within vesicles in the cytoplasma of the host. The chromatoplasma has 15–20 concentrically arranged thylakoids, plastoglobuli and phycobilisomes. The centroplasma contains polyhedral bodies. The theca of/Paulinella/ chromatophora is composed of rectangular scales arranged in a very regular manner. These scales exhibit a very complex ultrastructure. They are produced prior to cell division in large vesicles probably derived from cisternae of the only dictyosom which is located close to the nucleus in the aboral part of the thecamoeba. Microtubules may play a role in the morphogenesis of these scales. >> Hexagonal particles (virions?) are described from the nucleus and the cytoplasma of some of the thecamoebae. > > > This man Kies used cyanelle to name the plastid and it was tempting to use it too, but the more recent papers all use the term chromatophore so I used it too. I could revisit the term chromatophore stroma to make it chromatoplasma, but seeing as it is the equivalent of the chloroplast (etc) stroma that doesn't make any sense to me. Chromatoplasma has only ever been used in this one, 34 year old, publication. > > As I said this is a mess, but I'm not sure how else to handle the terms. If you have any suggestions I would welcome them! > > Let me know what you think, > > Andrea

Reported by: rachhuntley

Original Ticket: "geneontology/ontology-requests/5387":https://sourceforge.net/p/geneontology/ontology-requests/5387

emailed Debby Siegele asking for help

Original comment by: mah11

My communication with Michael Melkonian (Paulinella chromatophore expert) is pasted below;

Dear Rachael,

difficult questions! the term chromatophore is derived from Greek and means "color-bearer". It is a descriptive term that has been applied to three completely different (but colored) structures: (1) whole cells (the pigment cells in the skin of invertebrates and vertebrates). This term has apparently priority having been introduced in 1819 by an italian scientist. (2) organelles (the equivalent of plastids) introduced by Schmitz in 1883, and (3) membranes of bacteria containing photosynthetic pigments, introduced in 1952 by Stanier and colleagues (for pigment particles isolated from broken cells of the photosynthetic bacterium Rhodospirillum rubrum). Except for the pigment cells, the other two terms have gradually fallen out of use over the last decades. We re-introduced the term "chromatophore" for the intracellular, photosynthetic entities of Paulinella chromatophora (the term was originally used by Lauterborn in 1895 when he discovered the organism) for the reason to distinguish them from either cyanobacteria or plastids. In essence, the Paulinella chromatophore is a genetically highly reduced intracellular (endocytobiotic) cyanobacterium that is photosynthetically active and incapable of an independent existence outside its host. In its genome size it is intermediate cyanobacteria and plastids. We did not term the photosynthetic inclusions of Paulinella plastids, for two reasons: (1) they have a different phylogenetic origin than plastids (i.e. they were derived from a different type of cyanobacterium than the plastids), (2) they have not compartmentalized their photosynthesis genes between two genomes (the chromatophore and nuclear genomes) as plastids have. lace -I think the terms "vesicular chromatophore" and "organellar chromatophore" for the bacterial and Paulinella chromatophores respectively would make some sense. -I would place the Paulinella chromatophore as a derivative of (if more than one option is allowed) the terms "symbiosome" and "cyanobacteria", because it is essentially a genetically reduced, endocytobiotic cyanobacterium that performs the function of a photosynthetic "organelle" for its host. -of the chromatophore-related terms I would use as derivatives "C. thylakoid membrane, C. inner membrane, C. outer membrane, C. thylakoid lumen, C. thylakoid I don't think the terms C. membrane (which membranes? thylakoids or envelope membranes?) and C. stroma (the term stroma is linked to the term plastid, and, as mentioned above, we do not regard the chromatophores as plastids) are appropriate. Other terms that could be used as derivatives would be C. phycobilisomes, C. carboxysomes, and C. peptidoglycan.

With kind regards, Michael Melkonian

Dear Dr. Melkonian,

I wonder if you could help me. I work for the Gene Ontology Annotation group at the EBI, we maintain three ontologies of terms, Molecular Function, Biological Process and Cellular Component. We would like to enter some new terms in the Cellular Component ontology for the chromatophore of Paulinella but would like to ask you, as an expert on the subject, some questions to help clarify the naming and position of the terms in the ontology.

Currently, the Gene Ontology has a 'Chromatophore' term for the structure found in photosynthetic bacteria and cyanobacteria (see http://www.ebi.ac.uk/ego/GTerm?id=GO:0042716). The location of this term in the ontology is as a child of 'cytoplasm'.

We would like to add a term for the Paulinella chromatophore, which I believe is a photosynthetic plastid-like structure? There are several questions, firstly, we need an appropriate name for the term which should distinguish it from the bacterial chromatophore (unfortunately we cannot use 'Paulinella' in the term name as GO cannot have any species-specific information in the term names). One suggestion has been to name the bacterial chromatophore 'cellular chromatophore' (or maybe 'vesicular chromatophore') and the Paulinella chromatophore 'plastid chromatophore' - would this make sense to you?

Secondly is the position of the Paulinella term in the GO hierarchy, I understand from the literature that there is question of whether or not the Paulinella chromatophore is a plastid? Would it be incorrect to place the new term as a child of the GO term 'plastid' (see http://www.ebi.ac.uk/ego/GTerm?id=GO:0009536)? Another option is to place it as a child of 'symbiosome' (see http://www.ebi.ac.uk/ego/GTerm?id=GO:0043659), or maybe just as a child of 'cytoplasm'?

As you can see, we are a little confused, so any help you can give will be gratefully received!

Finally, further Paulinella chromatophore-related terms have been suggested, after reading an abstract by Kies (Protoplasma 80:69-89, 1974; PubMed 4208322); Chromatophore inner membrane, C. intermembrane space, C. membrane, C. outer membrane, C. stroma, C. thylakoid, C. thylakoid lumen and C. thylakoid membrane. In your opinion, are these appropriate child terms for the Paulinella chromatophore?

Once again, thank-you for taking time to read this, I do hope you can give us some advice.

Best wishes, Rachael Huntley.

Original comment by: rachhuntley

I've come back to this question after a while, and have made some executive decisions. Here's what I propose to do:

- Stop worrying about whether to group everything that is subcellular and called a chromatophore. Just make sure the terms we have avoid confusion. If people want a grouping term (e.g. 'subcellular photosynthetic chromatophore') we can add one later.

- rename terms: GO:0042176 chromatophore rename to 'plasma membrane-derived chromatophore'

GO:0042176 chromatophore membrane rename to 'plasma membrane-derived chromatophore membrane'

- Leave relationships for the above two terms as they are (because usage varies w.r.t. whether cyanobacterial thylakoids are called chromatophores -- I found literature & web sites both ways round -- and whoever did this bit of GO in the past may have known more than I do).

- Add 'organellar chromatophore', with synonym 'Paulinella-type chromatophore', for the Paulinella chromatophore; use same wording in terms for parts (lumen, membrane, etc.).

From PMID:18356055 and a discussion in the literature cited therein, I've got the impression that some researchers consider the Paulinella chromatophore to be an organelle, but others don't. For now, I'll go with the parentage suggested by Michael Melkonian and relayed by Rachael; if the community ever agrees that it's an organelle, we can move the terms.

I'm also using the 'symbiosome' parentage to word the definition: A bacteroid-containing symbiosome in which the bacterial component is a genetically highly reduced cyanobacterium that is photosynthetically active and incapable of an independent existence outside its host. The chromatophore functions as a photosynthetic organelle, and has been found and characterized in the amoeba Paulinella chromatophora. [PMID:18356055, GOC:expert_MM]

(Note: the reason I've opted not to use 'vesicular chromatophore' is that not all purple-bacterial chromatophores form complete vesicles.)

Let me know if this will work, m

Original comment by: mah11

assigned_to: nobody --> gomidori

Original comment by: mah11

Hi Midori,

This sounds sensible. I will contact the Swiss-Prot Subcell curators to see if they would consider changing the parentage of their chromatophore term (currently under plastid) to reflect ours and then I should be able to map it. Just to clarify, the child terms I want are the following; Chromatophore inner membrane, C. outer membrane, C. intermembrane space, C. membrane, C. thylakoid, C. thylakoid lumen and C. thylakoid membrane (C. stroma was not deemed appropriate).

Thanks, Rachael.

Original comment by: rachhuntley

added organellar chromatophore GO:0070111 organellar chromatophore membrane GO:0070112 organellar chromatophore inner membrane GO:0070113 organellar chromatophore outer membrane GO:0070114 organellar chromatophore intermembrane space GO:0070115 organellar chromatophore thylakoid GO:0070116 organellar chromatophore thylakoid lumen GO:0070117 organellar chromatophore thylakoid membrane GO:0070118

to avoid confusion with new terms, renamed: GO:0042716 'plasma membrane-derived chromatophore' GO:0042717 'plasma membrane-derived chromatophore membrane' [note - I mistyped the IDs for these terms in an earlier comment; they're correct here]

Please check the path up from the new organellar chromatophore terms -- I've followed the expert's advice to put them under symbiosome, but if that terms ancestors (including endocytic vesicle, which leads back to organelle anyway) look problematic, I can move the lot further up within the organelle branch any time.

Original comment by: mah11

status: open --> closed-accepted

Original comment by: mah11

geneontology / go-ontology

Chromatophore terms (Paulinella) #5369