ribulose bisphosphate carboxylase complex

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Hello

This issue was brought to my attention by TIGR annotator Scott Durkin.

Currently there is only one ribulose bisphosphate carboxylase complex term: "ribulose bisphosphate carboxylase complex" (GO:0009573)

This term is a child of "chloroplast stroma" (GO:0009570) and is therefore not appropriate for bacterial and archaeal genes. There will need to be terms specific for bacteria, eukaryotes and perhaps archaea so that the bacterial terms are not children of any organelles.

There is no definition for the current term, but it should be kept in mind when making the new terms that there are 3 forms of this complex currently known: Form I requires both large and small subunits and is found in bacteria and eukaryotes. Form II apears to require only large subunits and is found in bacteria and eukaryotes. Form III is found only in archaea and may only be composed of large subunits.

More info at PMID:12730164, Swiss-Prot:P50922, Swiss-Prot:P22849

Thanks for your time, Michelle

Reported by: mlgwinn

Original Ticket: "geneontology/ontology-requests/1466":https://sourceforge.net/p/geneontology/ontology-requests/1466

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Hi Michelle,

Sure, we can change the existing term to 'sensu Viridiplantae' (or whatever the best plant-y taxon would be), and add a generic parent term. I'm not sure how best to work in the form I/II/III business, since there's not a convenient one-to-one correspondence wth the 'sensu' terms we'd need. Any thoughts?

Also, what parent(s) should the new archaeal and bacterial terms have?

Midori

Original comment by: mah11

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Hi Midori,

Sorry for taking so long to get back to you on this.

The more I look at this stuff the more confused I get! I think I am out of my depth on this issue.

In an effort to find parent terms for the new bacterial and Archael ribulose bisphosphate carboxylase (RubisCO) complex terms I consulted my Atlas "Principles of Microbiology" text which says that RuBisCo lives on the thylakoid membranes of microorganisms. So that seemed like a good parent. But when I checked that term out, I found that there are more than one relevant term. Currently I find: "thylakoid (sensu Cyanobacteria)" GO:0030075 "thylakoid (sensu Proteobacteria)" GO:0030074 "thylakoid membrane" GO:0042651 Plus some other plant specific ones.

There is also the term: "chromatophore" GO:0042716

According to my Atlas text and to some info I found at a very informative Arizona State University site, I think there might be some problems with these terms. From my reading it seems that thylakoids are a specific, more specialized, kind of chromatophore. I don't think the photosynthetic membrane structures in the Proteobacteria are considered thylakoids they are simply chromoatophores.

So, two suggestions arise from this:

1. "thylakoid (sensu Cyanobacteria)" GO:0030075 should be a child of "chromatophore" GO:0042716
2. "thylakoid (sensu Proteobacteria)" GO:0030074 should be obsoleted.

Another concern I have is that in the tree structure for "thylakoid (sensu Viridiplantae)" it has "thylakoid membrane" as a child. I was wondering if the Cyanobacterial term should have the same "thylakoid membrane" child?

I can tell from the existence of the obsolete term "thylakoid (sensu Bacteria)" the someone has already been revising this section of the DAG and I certainly don't want to step on any toes here. Like I said, I'm out of my depth with this stuff.

A couple of final points.... there are other groups of photosynthetic bacteria not represented with the current terms: The green nonsulfur and green sulfur bacteria use their cytoplasmic membranes for photosynthesis, so I guess they don't need new terms. The Prochlorobacteria have thylakoids, so they would need their own term: "thylakoid (sensu Prochlorobacteria)"

Now, back to finding parents for the RubisCo complex terms..... To my knowledge there is not a breakdown of RubisCO complexes according to Cyanobacteria or Proteobacteria so I don't think there should be separate RubisCO terms for the two groups, but if there is not then I'm not sure what the parent should be. I guess it would be "chromatophore" even though for the Cyanobacteria that won't be quite specific enough and for the green bacteria it will be too specific.

Uhhh this is making my head hurt.....

Michelle

Original comment by: mlgwinn

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Hi Michelle,

do you know how many of these different kinds of organism are curently being annotated? If we have a relatively small number then maybe we could start by making terms that fit those?

Jen

Original comment by: jenclark

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Hi Michelle,

Do you have any idea of how I'd work out which organisms need terms made?

Jen

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Original comment by: jenclark

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Hi Jen, I'm checking into this (what's currently being annotated) and I'll get back to you as soon as I can. Michelle

Original comment by: mlgwinn

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Hi Michelle,

Did you have any luck finding out about that?

Thanks,

Jen

Original comment by: jenclark

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Ooops - I forgot to do this. Sorry about that - I sent an email to the team today - so hopefully I'll have some info soon. Michelle

Original comment by: mlgwinn

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Hi Jen,

It looks like we have representatives of most groups so here are my suggestions:

1. give "thylakoid (sensu Cyanobacteria)" GO:0030075 the additional parent "chromatophore" GO:0042716

2. I actually think "thylakoid (sensu Proteobacteria)" GO:0030074 should be obsoleted, but I hesitate to do this, knowing that someone put it there and thought it was correct. So, I'm not sure.

3. Create new term "ribulose bisphosphate carboxylase complex" as a child of "cytoplasm" (GO:0005737). Def: "A complex containing either both large and small subunits or just small subunits which carries out the activity of producing 3-phosphoglycerate from carbon dioxide and ribulose-1,5-bisphosphate." The same definition can be used for the children too I think, with the appropriate "as in the Cyanobacteria", etc.

4. The existing "ribulose bisphosphate carboxylase complex" (GO:0009573) should change to "ribulose bisphosphate carboxylase complex (sensu Viridiplantae)" (or other plant sensu group) and get the additional parent of the new term from #3.

5. New term: "ribulose bisphosphate carboxylase complex (sensu Cyanobacteria)" as a child of "thylakoid (sensu Cyanobacteria)" (GO:0030075) and as a child of new term from

   3.

6. New term: "ribulose bisphosphate carboxylase complex (sensu Green and Purple bacteria)" as a child of "chromatophore" GO:0042716 and new term #3.

7. Change definition of "chromatophore" GO:0042716 to be a bit more general. According to my Atlas book it is "Internal membranes in some photosynthetic bacteria that contain the pigments and accessory molecules utilized in photosynthesis."

This would solve all the issues I think. Let me know your thoughts on these suggestions.

Thanks, Michelle

Original comment by: mlgwinn

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Hi Michelle,

Thanks for getting all that worked out and so clearly explained. I think for:

3. Create new term "ribulose bisphosphate carboxylase complex" as a child of "cytoplasm" (GO:0005737). Def: "A complex containing either both large and small subunits or just small subunits which carries out the activity of producing 3-phosphoglycerate from carbon dioxide and ribulose-1,5-bisphosphate." The same definition can be used for the children too I think, with the appropriate "as in the Cyanobacteria", etc.

we actually need defs that talk about the subunits more and not about the reaction. As in:

DNA-dependent protein kinase complex ; GO:0005958 def: A large protein complex which is involved in the repair of DNA double- strand breaks and V(D)J recombination events. In mammals, it consists of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), the DNA end-binding heterodimer, Ku, the nuclear phosphoprotein XRCC4 and DNA ligase IV.

Do you have this information for the generic one and for the sensu versions you want? Or if not do you have PMID reference for the papers?

I wrote to Midori to ask about the one you thought might be worth obsoleting since her initials are in the def reference box. I will also write to the list just in case there's anyone else out there who's affected by this.

Thanks,

Jen

Original comment by: jenclark

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Hi Michelle,

Midori, Kirril and Leonore Reiser made the term in no.2. Kirill is going to comment on your suggestion when he gets back from his holiday.

Thanks,

Jen

Original comment by: jenclark

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Jen forwarded some very old email exchange re. photosynthetic apparatus. The essence is that some authors did use the term "thylakoid" in conjunction with purple photosynthetic bacteria (see e.g. PMID:3890891; PMID:4545071), who happen to belong to Proteobacteria. I do not know how widespread this practice is, but I suspect that most biologists think of thylakoids in cyanobacteria and chloroplast only. Not all Proteobacteria are photosynthetic and therefore generic term for Proteobacterial thylakoid may make little sense. Taxonomically the situation is complicated (see e.g. http://141.150.157.117:8080/prokPUB/chaphtm/239/01\_00.ht m for a good review): "purple nonsulfur bacteria" and "purple sulfur bacteria" are not monophyletic groups. How can we go around it? Will the term "sensu photosynthetic Proteobacteria" suffice or not?

Kirill

Original comment by: kiri11

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Hi guys....sorry for my very VERY late arrival on this one, I looked to confirm that ZFIN does not have genes annotated to the 'ribulose-bisphosphate carbolylase activity' or '...complex' terms. In fact we do... This appears to be generated thru interpro2go translation from IPR000685. The current placement of the RuBisCo complex term (GO:0009573) places it squarely in chloroplasts (not found in zebrafish of course). SOoo...either the new complex and activity terms need to take us vertebrates into account and/or the interpro2go mapping needs adjustment.

Original comment by: doughowe

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Hi Doug,

I was just reading this thread when I reached your comment. When we do INTERPRO to GO mapping here at TAIR, we frequently get mappings to terms that make no sense for plants, for example, we had mappings to terms like "xxxx (sensu Bacteria)" or "perception of smell" or "cholesterol transport" (plants don't make cholesterol). So while the sequence similarity does exist, we manually screen out these types of IEA annotations as they are very likely spurious and not relevant for plants. (Plus it kind of freaks our users out to see their genes annotated to 'visual perception' ;-) )

What's my point? Since Rubisco is involved in carbon fixation during photosynthesis and (as far as I know) zebrafish don't photosynthesize, you may want to drop these annotations instead of modifying the GO structure to accommodate vertebrates.

My 2 cents,

Tanya

Original comment by: tberardini

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Hi Michelle and Jen,

As far as the proposed changes for the existing term go (#4 of Michelle's plan below), this looks fine for our purposes.

Go for it! (no pun intended ;-> )

Tanya

Original comment by: tberardini

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I'm leaving rubisco to the plant experts ;)

... but these recent comments suggest that some of the Interpro2go mapppings should have another look. I've set up a bit of the Annotation tracker for that sort of thing.

m

Original comment by: mah11

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Tanya, I looked around a bit and agree that zebrafish have no need for being annotated to RuBisCo terms. If Midori didn't already do it, I'll make an entry in the SF tracker to get the mappings modified. -Doug

Original comment by: doughowe

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In response to Kirill,

The NCBI taxonomy entry for

Proteobacteria Taxonomy ID: 1224 http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi? mode=Info&id=1224&lvl=3&lin=f&keep=1&srchmode=1&unlock

lists purple photosynthetic bacteria as one of the common names. I wonder if we could make up sensu taxon to cover this as Kirill suggests?

Jen

Original comment by: jenclark

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I Just checked with Michael Ashburner about how to deal with the sensu Proteobacteria and he says it doesn't matter that not all the proteobacteria have that characteristic, and that we can use the sensu grouping anyway. I think that means we can just leave that term as it is.

Jen

Original comment by: jenclark

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The objection I had was not that not all Proteobacteria are photosynthetic, but rather that my understanding is that the photosynthetic structures in Proteobacteria are not thylakoids. As Kirill said below, I believe that term is used in Cyanobacteria, but not Proteobacteria - that is what my Atlas microbiology text says. The structure in the Proteobacteria is much simpler, it would be considered just a chromatophore. Michelle

Original comment by: mlgwinn

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Everybody seems quite happy with everything Michelle's suggested except for number 2 where her question has not yet been answered, so I'll implement everything except number 2.

Jen

Original comment by: jenclark

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I have done these bits:

1. gave "thylakoid (sensu Cyanobacteria)" GO:0030075 the additional parent "chromatophore" GO:0042716

2. Created new term "ribulose bisphosphate carboxylase complex" as a child of "cytoplasm" (GO:0005737). Def: "A complex containing either both large and small subunits or just small subunits which carries out the activity of producing 3-phosphoglycerate from carbon dioxide and ribulose-1,5-bisphosphate." The same definition is used for the sensu children below, with the appropriate endings.

3. The existing "ribulose bisphosphate carboxylase complex" (GO:0009573) changed to "ribulose bisphosphate carboxylase complex (sensu Magnoliophyta)" since this is what its parentage represents and it is undefined. Given the additional parent of the new term from #3.

4. New term: "ribulose bisphosphate carboxylase complex (sensu Cyanobacteria)" as a child of "thylakoid (sensu Cyanobacteria)" (GO:0030075) and as a child of new term from

   3.

5. New term: "ribulose bisphosphate carboxylase complex (sensu Proteobacteria)" as a child of "chromatophore" GO:0042716 and new term #3.

Term numbers:

GO:0048492 ; ribulose bisphosphate carboxylase complex GO:0048493 ; ribulose bisphosphate carboxylase complex (sensu Cyanobacteria) GO:0048494 ; ribulose bisphosphate carboxylase complex (sensu Proteobacteria)

I haven't done no.2 yet and I haven't worked out the sensu designation for green bacteria yet. Also I didn't do no. 7 because the change in def seemed a bit radical. It seemed to be changing from saying the chromatophore was a vesicle to saying it was a membrane and I think that might need an obsoletion and a change in parentage. I thought I'd hang fire on that one and ask just how much more general you wanted the def to be.

Do you have any thoughts on these things?

Thanks,

Jen

Original comment by: jenclark

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Hi,

How about this for the def of chromatophore:

"A pigment bearing structure found in certain photosynthetic bacteria and cyanobacteria which is derived from the cytoplasmic membrane, sometimes consisting of simple invaginations and sometimes a complete vesicle."

That's a combination of the current definition and the one from my Atlas book.

Regarding number 2 - I have done more research on this and everywhere I look the term "thylakoid" is used with the cyanobacteria (and plants) but not with the proteobacteria, other terms are used for the proteos. I think Kirill's remarks below agree with this - I quote "but I suspect that most biologists think of thylakoids in cyanobacteria and chloroplast only". Again, my Atlas text is pretty clear on the distinction, there is a table indicating characteristics of photoautotrophic microorganisms and thylakoid is used only for the Cyanobacteria, Prochloron, and algae. I think there are no genes annotated to the term currently. I think it should be obsoleted.

Michelle

Original comment by: mlgwinn

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Hi Michelle,

I had a think about the options and just did this for the sensu green and purple bacteria term in the end. I think it will really be the best thing for annotators, and shouldn't be a problem for the sensu rules.

ribulose bisphosphate carboxylase complex (sensu Proteobacteria, Chloroflexaceae and Chlorobiaceae) def: A complex containing either both large and small subunits or just small subunits which carries out the activity of producing 3-phosphoglycerate from carbon dioxide and ribulose-1,5-bisphosphate. As in, but not restricted to: the purple bacteria and relatives (Proteobacteria, ncbi_taxonomy_id:1224), the filamentous anoxygenic phototrophic bacteria (Chloroflexaceae, ncbi_taxonomy_id:1106), and the green sulfur bacteria (Chlorobiaceae, ncbi_taxonomy_id:191412).

Jen

Original comment by: jenclark

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chromatophore ; GO:0042716

changed def: "A membrane enclosed\, pigment-bearing vesicle found in certain photosynthetic bacteria and cyanobacteria\, derived from invagination of the cytoplas mic membrane." [PMID:11867431, ISBN:0395825172, GO:jl]

to:

def: "A pigment bearing structure found in certain photosynthetic bacteria and cyanobacteria which is derived from the cytoplasmic membrane\, sometimes consisting of simple invaginations and sometimes a complete vesicle." [PMID:11867431, ISBN:0395825172, GO:jl]

Original comment by: jenclark

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Hi Michelle,

Thanks for looking further into the obsoletion one. I was thinking how to write the comment and I'm not sure that we have a replacement terms for this. Shall I just direct annotators to the children of chromatophore ; GO:0042716 and if they need a more exact term then I can make it when the annotation need is more specific?

Jen

Original comment by: jenclark

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Hi Jen,

I think directing users to "chromatophore" and its children is the best thing - and I agree new terms can be made if needed. I have not found a more specific term for the structures in theProteobacteria other than "chromatophore"...

I'm glad you were able to get both the purples and greens into the sensu string - thanks for that and all your help on this.

Michelle

Original comment by: mlgwinn

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Hi Michelle,

I have obsoleted "thylakoid (sensu Proteobacteria)" GO:0030074 with comment: This term was made obsolete because thylakoids are not found in organisms of the Phylum Proteobacteria. To update annotations\, consider the biological process term 'chromatophore ; GO:0042716' and its children.

I think that's everything done now. Shall I close this page?

Jen

Original comment by: jenclark

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Hi Jen,

Yes, I think that takes care of everything - this one can be closed.

Thanks again for all of your help.

Michelle

Original comment by: mlgwinn

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• status: open --> closed-accepted

Original comment by: jenclark

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

Original comment by: jenclark

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Hi Michelle,

Amelia just pointed out that these terms

GO:0030078: light-harvesting complex, core complex GO:0030079: light-harvesting complex, peripheral complex GO:0030090: reaction center (sensu Proteobacteria)

were previously children of

GO:0030074 ; thylakoid (sensu Proteobacteria)

Do you think they are okay just to be left with the other parents that they still have or should I give them additional parents?

Thanks,

Jen

Original comment by: jenclark

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Oh no - just when I thought this one was all done! Thanks Amelia for catching this - clearly I did not pay attention to the children of these terms - sorry about that.

I think these terms can not stay where they are in the tree since one of their grandparents is "thylakoid" and they are not in thylakoids (as we just obsoleted their specific thylakoid parent). So, I will have to look into this more closely and also to the children of the other terms that were involved in this.

I'll get back to you with suggestions later today (I hope).

Michelle

Original comment by: mlgwinn

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OK here is my suggestion for these: "light-harvesting complex (sensu Proteobacteria)" (GO:0030077) and its children should be children of "chromatophore" (GO:0042716). Currently, the generic light-harvesting complex parent is under 'thylakoid" and that does not work for the Proteobacteria, so I guess the generic term should be moved out to "intracelluar" and its other children ("light-harvesting complex (sensu Viridiplantae)" (GO:0009503) and"phycobilisome" (GO:0030089)) should get second parents under "thylakoid".

Will that work?

Michelle

Original comment by: mlgwinn

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That's great. :-) Thanks Michelle.

Jen

Original comment by: jenclark

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Original comment by: jenclark

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"light-harvesting complex (sensu Proteobacteria)" (GO:0030077) and its children are now children of "chromatophore" (GO:0042716). The generic light-harvesting complex term has been moved out of under thylakoid to be a child of intracellular GO:0005622. The generic term's two children ("light-harvesting complex (sensu Viridiplantae)" (GO:0009503) and"phycobilisome" (GO:0030089)) still have 'thylakoid' as an ancestor via another relationship so I did not add that parentage.

This item is finished now so I'll close it.

Thanks,

Jen

Original comment by: jenclark