Difference between revisions of "Meeting Notes 3"

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(sporulation)
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'''Questions:'''<br>
 
'''Questions:'''<br>
 
 
What are the distinguishing features of sporulation in different species?<br>
 
What are the distinguishing features of sporulation in different species?<br>
  
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GO:0030435 sporulation
 
GO:0030435 sporulation
  
Sexual or meiotic spores
+
*Sexual or meiotic spores
 
 
Ascospores
+
** Ascospores (meiotically produced spores form by Ascomycetes)
  
+
** Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia.  From Wikipedia)
Basidiospores (A haploid sexual spore formed on a basidium following the process of karyogamy and meiosis. Dr. Fungus) (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia.  From Wikipedia)
 
  
Zygomycetes (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)
+
** Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)
  
 
 
Asexual or mitotic spores
+
*Asexual or mitotic spores
 
 
Arthrospores (aka oidia) (A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum. Dr. Fungu ) (Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)
+
**Arthrospores (aka oidia) (A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum. Dr. Fungu ) (Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)
 
+
 +
**Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)
 +
 +
**Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation.  Prescott)
 
 
Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)
+
**Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes)
 
 
 
 
Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott)
+
**Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip.  Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia):    An asexual sac-like cell that has its entire content cleaved into sporangiospores.
 
+
 +
**Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some Gram-positive bacteria)
 +
 +
**Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)
 
 
Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (An asexual, non-motile, usually deciduous propagule that is not formed by cytoplasmic cleave, free-cell formation, or by conjugation. Dr. Fungus) (asexual spores formed by Ascomycetes)
+
**Myxospore
  
+
**Dictyostelium
Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip.  Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall)
 
Sporangium (pl. sporangia):    An asexual sac-like cell that has its entire content cleaved into sporangiospores.
 
 
 
 
 
 
Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some Gram-positive bacteria)
 
 
 
 
Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)
 
 
 
 
Myxospore
 
 
 
 
 
Dictyostelium
 
 
 
 
Physarum?
 
  
 
==proteasome==
 
==proteasome==

Revision as of 07:29, 20 February 2008

Electron transport

Electron transport


sporulation

sporulation (sensu Bacteria)
sporulation (sensu Fungi)
spore development (sensu Magnoliophyta)

People:

Val
Maria Costanzo
Michelle
Midori
Pascale
Jen
Jim Hu
Tanya
Debby Siegele

Questions:
What are the distinguishing features of sporulation in different species?

Plan:

Michelle speaking - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.

Eurie is to be included in one of these calls so she can get up to speed on editing techniques.

Debby Siegele (Texas A&M) (Nov 25): I think that the child terms for sporulation (GO:0030435) need to be reorganized. The current organization is shown below. A proposed reorganization is shown following my discussion of the current terms.

  • GO:0030435: sporulation
    • GO:0030436: sporulation (sensu Bacteria)
      • GO:0042243: spore wall assembly (sensu Bacteria)
    • GO:0042173: regulation of sporulation
    • GO:0042244: spore wall assembly
    • GO:0048622: reproductive sporulation (def: "The formation of reproductive spores." [GOC:jic])
      • GO:0030437: sporulation (sensu Fungi)
        • GO:0048315 : conidium formation
        • GO:0031321 : prospore formation
        • GO:0030476 : spore wall assembly (sensu Fungi)


The term for sporulation (sensu Bacteria) and spore wall assembly (sensus Bacteria) should be eliminated because there are multiple types of bacterial spores (e.g. endospores, exospores, myxospores, and akinetes) and therefore multiple types of spore cell walls and assembly pathways. The term GO:0055030: peptidoglycan-based spore wall (a child term of spore wall) could be retained as it refers to a specific type of spore wall.

I would make the same argument for eliminating the term for sporulation (sensu Fungi) as different groups of fungi make spores differently. (In fact, the synonyms listed for sporulation (sensu Fungi) are specific for formation of ascospores, which excludes fungi outside the Ascomycetes.) I suspect that the terms spore wall (sensu Fungi) (GO:0005619) and spore wall assembly (sensu Fungi) should also be eliminated, since there probably isn't a common spore wall present in all fungal spores, but I don't know enough about this.

I don't know is meant by a reproductive spore. Does this refer to the spore being formed by a sexual process? or that the spores themselves are gametes (as is the case with some fern spores)? or simply that the spores will rise to a new organism? If the first is correct, then GO:0048315 shouldn't be a child term of reproductive spore, since conidia are asexual spores and the true path rule isn't followed.

I saw that one of the parent terms for reproductive sporulation is GO:0022413: reproductive process in single-celled organism. Does "single-celled" refer to spore itself? or to the organism that produces the spores?

A possible reorganization would be

  • GO:0030435: sporulation
    • GO:0042173: regulation of sporulation
    • GO:0042244: spore wall assembly
    • new GO term: formation of asexual spores
      • GO:0048315: conidium formation
      • new GO term: endospore formation
    • new GO term: formation of sexual (meiotic) spores (or redefinition/clarification of GO:0048622: reproductive sporulation?)
      • GO:0030437: redefined as ascospore formation

In AmiGO, the only genes annotated to GO:0030437: sporulation (sensu Fungi) are from S. cerevisiae and S. pombe. These are both Ascomycetes, so the change in definition wouldn't affect these annotations. Among the model organism databases, the only other organism I found with genes annotated to GO:0030437 is Dictyostelium discoidium. DictyBase has 4 genes (geneDDB0230045, geneDDB0234013, rasC, and rasD) annotated to sporulation (sensu Fungi). The annotations were inferred from electronic annotation.

Midori (Jan. 4, 2008): I have implemented the changes to fungal-type cell wall and spore wall terms as described in the notes from Nov. 2. (I have not tried to mess with the sporulation process terms, but Debby's suggestions sound reasonable. I lean toward renaming GO:0030437 and rewording its definition such that it refers to ascospore formation, because that's been the implicit meaning given who worked on it, what we were thinking of, and how it's been used.)

Notes added Feb. 14, 2008 (Midori)

(very) rough draft of possible structure:

Please comment on this -- should any more terms be included, or anything shown be left out? I fully expect more than one round of comments before it's resolved!

sporulation GO:0030436
[i] reproductive sporulation GO:0048622 (rename 'formation of sexual (meiotic) spores'? should we add any children, such as these:
--[i] fern-type sporulation?
--[i] moss-type sporulation?
[i] ascospore formation GO:0030437 (renamed)
--[p] ascospore wall formation GO:0030476 (renamed)
--[p] prospore formation GO:0031321 (may need to be renamed because the definition seems more specific than the name, but I haven't thought of a new name yet)
[i] (a term for basidomycete sporulation) GO:new
[i] conidium formation GO:0048315
--[p] conidium wall assembly GO:new (or "formation" instead of "assembly")
[i] endospore formation GO:new
--[p] endospore wall assembly GO:new
[i] exospore formation GO:new
--[p] exospore wall assembly GO:new
[i] myxospore formation GO:new
--[p] myxospore wall v GO:new
[i] akinete formation GO:new
--[p] akinete wall assembly GO:new
[p] spore wall assembly GO:0042244
--[i] ascospore wall formation GO:0030476 (renamed)
--[i] conidium wall assembly GO:new
--[i] endospore wall assembly GO:new
--[i] exospore wall assembly GO:new
--[i] myxospore wall v GO:new
--[i] akinete wall assembly GO:new
[p] regulation of sporulation GO:0042173

We can also add "xx spore wall" terms to the cellular component (CC) ontology.

note: we have "peptidoglycan-based spore wall" in CC (GO:0055030); does it correspond to any of the wall types listed above?

To be made obsolete:

- sporulation (sensu Bacteria) GO:0030436
- spore wall assembly (sensu Bacteria) GO:0042243

Some existing definitions should be rewritten. Two that I've had a stab at so far:

sporulation GO:0030436
def: The process by which a relatively unspecialized cell acquires the specialized features of a spore. [can include general description of features shared by all spores]

ascospore formation GO:0030437
def: The process by which a diploid cell undergoes meiosis, and the meiotic products acquire the specialized features of an ascospore [include ascospore features here].

Additional comments:

  • Reproductive sporulation
    • David: I don't think it was necessarily meant to be just meiotic. I think it means 'sporulation whose primary biological objective is reproduction' as opposed to 'sporulation whose primary biological objective is that of protection'. I think it was the fungal groups who worked on this part of the graph. Does it make sense that they would think of sporulation as primarily a reproductive process while you folks would think of it as a protective process? The latter distinction was entirely mine based on reading a textbook.
    • Midori: David remembers more of this than I do; I would have just said I don't know where the "reproductive sporulation" term came from! We should check again with fungal experts, because in S. cerevisiae sporulation occurs in diploids in response to nutrient starvation (specifically nitrogen, if I recall correctly); it's not as obviously coupled to reproduction as in ferns or some other fungi, e.g. mushrooms. Back in my lab days I tended to think of cerevisiae sporulation as more protective than reproductive, although four spores are produced so it's got a bit of reproductive character. Sporulation in ferns and mosses would certainly fit under "reproductive sporulation"; I don't know anything more about them, such as distinguishing features or whether we would need one term or more. We should discuss whether to keep the "reproductive sporulation" term; if so, whether to change its name, what (if any) children it should have, whether to add a sibling for "sporulation in response to stress", etc.
    • Pascale: I think we should use sexual and asexual to distinguish meiotic and mitotic spores. As far as I know, all spoulation is a form of reproduction. Plus there are no direct associations to 'reproductive sporulation'. This is also consistent with the definition of reproduction: 'The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.'
    • 'Michelle: All sporulation is not reproductive. Sporulation in bacteria does not result in a net increase in the number of organisms - one cell becomes a spore and then germinates into one cell again. Sporulation in bacteria is generally a means to survive adverse conditions. So, if asexual sporulation will refer to a reproduction process, we will

still need some kind of non-reproductive sporulation term.

  • Jim: I think there is a problem with the fungal sporulation terms excluding or misrepresenting the basidomycetes by being marked as synonymous with ascospore processes.
    Midori: I think the apparent exclusion of basidomycetes will be addressed by renaming the existing "fungal" sporulation term and adding new terms.
  • Jim: The myxospores mentioned above by Debby are made by the Myxococcales. The model organism for them is Myxococcus xanthus, and their mod is at http://xanthusbase.org. I'm trying to help them with a clade-specific cluster of MODs project right now. In an oversimplified description, myxo is sort of a bacterial version of dicty. There is social behavior followed by aggregation into a multicellular fruiting body that differentiates into spores. Some of these are quite lovely. Via googling:
http://www.mbio.ncsu.edu/MB451/lecture/deltaEpsilonPurples/lecture.html

Debby 2/20/08 GO:0030435 sporulation

  • Sexual or meiotic spores
    • Ascospores (meiotically produced spores form by Ascomycetes)
    • Basidiospores (is a reproductive spore produced by Basidiomycete fungi. Basidiospores typically each contain one haploid nucleus that is the product of meiosis, and they are produced by specialized fungal cells called basidia. From Wikipedia)
    • Zygospores (Zygomycota, or zygote fungi, are a phylum of fungi. The name of the phylum comes from zygosporangia, where resistant spherical spores are formed during sexual reproduction. From Wikipedia)


  • Asexual or mitotic spores
    • Arthrospores (aka oidia) (A conidium formed by the modification of a hyphal cell(s) and then released by the fragmentation-lysis of a disjunctor cell or by fission through a thickened septum. Dr. Fungu ) (Hypha fragment through splitting of the cell wall to form cells that behave as spores. Prescott ) (asexual spores formed by Basidiomycetes)
    • Blastospores (Spores produced from a vegetative mother cell by budding. Prescott) (produced by Candida, produced by fungi in the class Glomeromycota, others?)
    • Chlamydospores (Spores produced by hyphal fragmentation that are surrounded by a thick wall before separation. Prescott)
    • Conidia (Spores produced at the tips or sides of a hyphae, but are not enclosed in a sac. Prescott) (asexual spores formed by Ascomycetes)
    • Sporangiospores (Asexual Spores that develop with a sac (sporangia) at a hyphal tip. Prescott) (A spore that is formed by a cleavage process following karyogamy and mitosis in a sporangium. Dr. Fungus) (produced by fungi in the class Chytridiomycota, differ from conidia in being surrounded by a second wall) Sporangium (pl. sporangia): An asexual sac-like cell that has its entire content cleaved into sporangiospores.
    • Endospore (Dormant, highly resistant spore with a thick wall that forms within another cell, produced by some Gram-positive bacteria)
    • Akinete (An akinete is a thick-walled dormant cell derived from the enlargement of a vegetative cell.[1] It serves as a survival structure. It is a resting cell of cyanobacteria and unicellular and filamentous green algae. [2] Under magnification, akinetes appear thick walled with granular-looking cytoplasms.)
    • Myxospore
    • Dictyostelium

proteasome

proteasome core complex (sensu Eukaryota)
cytosolic proteasome core complex (sensu Eukaryota)
proteasome regulatory particle (sensu Eukaryota)
cytosolic proteasome regulatory particle (sensu Eukaryota)
proteasome regulatory particle, base subcomplex (sensu Eukaryota)
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota)
proteasome regulatory particle, lid subcomplex (sensu Eukaryota)
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota)
proteasome complex (sensu Eukaryota)
cytosolic proteasome complex (sensu Eukaryota)
proteasome core complex (sensu Bacteria)
proteasome core complex, alpha-subunit complex (sensu Eukaryota)
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota)
proteasome core complex, beta-subunit complex (sensu Eukaryota)
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota)
proteasome regulatory particle (sensu Bacteria)

Also see SF 1848103

People:

Rama
Jim Hu
Michelle
Kate Dreher (TAIR)
Tanya

Questions:

Plan:

1. Merge ‘proteasome core complex (sensu Eukaryota)’ and ‘proteasome core complex (sensu Bacteria)’. Final term name = ‘proteasome core complex’ with improved, nice and generic definition: A multisubunit barrel shaped endoprotease complex, which is the core of the proteasome complex.

2. Drop (sensu Eukaryota) from ‘proteasome complex (sensu Eukaryota)’. Final term name = ‘proteasome complex’ with improved definition: A large multisubunit complex which catalyzes protein degradation. This complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.

3. Obsolete ‘proteasome regulatory particle (sensu Bacteria)’. The current definition says: A multisubunit complex that recognizes and unfolds ubiquitinated proteins, and translocates them to the core complex in an ATP dependent manner. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2). The problem is that there is no ubiquitin in bacteria and they don’t have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase (PAN), which we should have a new term for (see next item).

4. New term: ‘proteasome –activating nucleotidase’, def: A multisubunit complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner. Synonym: PAN

5. Drop (sensu Eukaryota) from ‘cytosolic proteasome core complex (sensu Eukaryota)’ and ‘proteasome regulatory particle (sensu Eukaryota)’. Retain current definitions and synonyms, just remove the ref to the taxon id.

6. Drop (s E) from ‘cytosolic proteasome regulatory particle (sensu Eukaryota)’ and improve definition from

The regulatory subcomplex of a proteasome located in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).

To

A multisubunit complex located in the cytosol of a cell, which caps one or both ends of the proteasome core complex. This complex recognizes, unfolds ubiquitinated proteins and translocates them to the proteasome core complex.

7. Drop (s E) from ‘cytosolic proteasome complex (sensu Eukaryota)‘ and improve definition from

A proteasome found in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).

To

A proteasome complex found in the cytosol of a cell.


8. Drop (s E) from ‘proteasome regulatory particle, base subcomplex (sensu Eukaryota)’ and improve definition from

Refers to the subunits of the regulatory particle that directly associates with the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).

To

Refers to the subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.

9. Drop (s E) from ‘proteasome regulatory particle, lid subcomplex (sensu Eukaryota)’ and improve definition from Refers to the subunits of the regulatory particle that forms the peripheral lid, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).

To

Refers to the subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.

10. Drop (s E) from ‘proteasome core complex, alpha-subunit complex (sensu Eukaryota)’ and improve definition from

Refers to the subunits that constitute the outer rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).

To

Refers to the proteasome core subcomplex that constitutes the two outer rings of the proteasome core complex.

11. Drop (s E) from ‘proteasome core complex, beta-subunit complex (sensu Eukaryota)’ and improve definition from

Refers to the subunits that constitute the inner rings of the proteasome core complex, as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).

To

Refers to the proteasome core subcomplex that constitutes the two inner rings of the proteasome core complex.

12. The remaining terms (cytosolic blah, blah, blah) just need the (s E) dropped from their term names and the defs improved to reflect the defs of their parent terms.

13. Need new term for grouping the ‘regulatory particle’ , ‘PAN’ and ‘proteasome activator complex’ (existing term with no relationship to proteasome right now. Kate and I thought of something like ‘proteasome attachment OR proteasome accessory OR proteasome accessory complex OR proteasome added stuff (ok, not the last one) with a definition something like:

‘A single or multisubunit complex, which caps one or both ends of the proteasome core complex and regulates entry into or exit from the proteasome core complex.’ I hate this definition. HELP!

(partial graph below, not is_a complete, you should be able to sort it out pretty easily in OBOedit)

   proteasome complex
   --[p]proteasome core complex
   ----[p]alpha
   ----[p]beta
   --[p]proteasome attachment/accessory/accessory complex (GO:new)
   ----[i]proteasome regulatory particle
   ------[p]base
   ------[p]lid
   ----[i]PAN (GO:new)
   ----[i]proteasome activator complex

The edits have been made and are being held in a branch file. The branch occurred at cvs version: $Revision: 5.631 $ of gene_ontology_edit.obo.

The branch is at http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/proteasome.obo.

An obsoletions warning mail has been sent.


Commit occurred on 15th January 2008 with addition of new terms:


[Term]
id: GO:0022624
name: proteasome accessory complex
namespace: cellular_component
def: "A protein complex, that caps one or both ends of the proteasome core complex and regulates entry into, or exit from, the proteasome core complex." [GOC:mtg_sensu, GOC:proteasome]
is_a: GO:0043234 ! protein complex
relationship: part_of GO:0000502 ! proteasome complex

[Term]
id: GO:0022625
name: cytosolic large ribosomal subunit
namespace: cellular_component
alt_id: GO:0005842
alt_id: GO:0009282
alt_id: GO:0030498
alt_id: GO:0030872
def: "The large subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]
synonym: "50S ribosomal subunit" NARROW []
synonym: "60S ribosomal subunit" NARROW []
synonym: "cytosolic large ribosomal subunit (sensu Archaea)" NARROW []
synonym: "cytosolic large ribosomal subunit (sensu Bacteria)" NARROW []
synonym: "cytosolic large ribosomal subunit (sensu Eukaryota)" NARROW []
synonym: "eukaryotic ribosomal LSU" NARROW []
synonym: "prokaryotic large ribosomal subunit" NARROW []
is_a: GO:0015934 ! large ribosomal subunit
is_a: GO:0044445 ! cytosolic part
relationship: part_of GO:0022626 ! cytosolic ribosome

[Term]
id: GO:0022626
name: cytosolic ribosome
namespace: cellular_component
alt_id: GO:0005830
alt_id: GO:0009281
alt_id: GO:0030871
def: "A ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]
synonym: "70S ribosome" NARROW []
synonym: "80S ribosome" NARROW []
synonym: "cytosolic ribosome (sensu Archaea)" NARROW []
synonym: "cytosolic ribosome (sensu Bacteria)" NARROW []
synonym: "cytosolic ribosome (sensu Eukaryota)" NARROW []
is_a: GO:0005840 ! ribosome
is_a: GO:0044445 ! cytosolic part

[Term]
id: GO:0022627
name: cytosolic small ribosomal subunit
namespace: cellular_component
alt_id: GO:0005843
alt_id: GO:0009283
alt_id: GO:0030499
alt_id: GO:0030873
def: "The small subunit of the ribosome that is found in the cytosol of the cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components." [GOC:mtg_sensu]
synonym: "30S ribosomal subunit" NARROW []
synonym: "40S ribosomal subunit" NARROW []
synonym: "cytosolic small ribosomal subunit (sensu Archaea)" NARROW []
synonym: "cytosolic small ribosomal subunit (sensu Bacteria)" NARROW []
synonym: "cytosolic small ribosomal subunit (sensu Eukaryota)" NARROW []
synonym: "eukaryotic ribosomal SSU" NARROW []
synonym: "prokaryotic small ribosomal subunit" NARROW []
is_a: GO:0015935 ! small ribosomal subunit
is_a: GO:0044445 ! cytosolic part
relationship: part_of GO:0022626 ! cytosolic ribosome

[Term]
id: GO:0022628
name: chloroplast large ribosomal subunit
namespace: cellular_component
def: "The large subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]
is_a: GO:0000311 ! plastid large ribosomal subunit
relationship: part_of GO:0043253 ! chloroplast ribosome

[Term]
id: GO:0022629
name: chloroplast small ribosomal subunit
namespace: cellular_component
def: "The small subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]
is_a: GO:0000312 ! plastid small ribosomal subunit
relationship: part_of GO:0043253 ! chloroplast ribosome


cytosolic ribosome

cytosolic large ribosomal subunit (sensu Eukaryota)
cytosolic large ribosomal subunit (sensu Archaea)
cytosolic large ribosomal subunit (sensu Bacteria)
cytosolic ribosome (sensu Archaea)
cytosolic ribosome (sensu Bacteria)
cytosolic ribosome (sensu Eukaryota)

cytosolic small ribosomal subunit (sensu Archaea)
cytosolic small ribosomal subunit (sensu Bacteria)
cytosolic small ribosomal subunit (sensu Eukaryota)


People:

Harold
Michelle
Jim Hu

Questions:

Can we also address this at the same time? SF1828366

Plan:


From Harold's e-mail:


The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s.
These are generated from post-transcriptional processing of a single rRNA precursor. Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt)
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are
post-transcriptionally processed from a single rRNA precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA
polymerase III, whereas the large transcript containing the other three is synthesized by RNA polymerase I. The large rRNA, typically called “28s”, is in
fact much larger than it's bacterial counterpart (~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes
contain 70-80 proteins.
I would think that the most single feature is the 3 vs 4 chain.
Although basically, mitochondrial ribosomes are thought to be “prokaryote-like”, some fungal and animal
mitochondrial ribosomes lack 5 sRNA, and are thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then
you would b safe).
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have
an intermediate number of proteins, etc. The expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together.
I propose
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope.
Although I wouldn't be adverse to using “5.8s-containing ribosome vs ??).
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference. The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be
small subunit of a three-chain containing ribosome
smll subunit of a four-chain containg ribosome.

References:
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and
Lewin, Genes VII ISBN:019879276-X

The Ribosome, ISBN:0879696206




Find previous notes from e-mail.

Note that the 5.8S rRNA in eukaryotes corresponds to a segment of the large (23S) rRNA in prokaryotes. I have a problem with splitting the ribosomes along the sensu terms or based on the number of rRNAs, since the ontology has already divided cytosolic from organellar ribosomes. I may be misunderstanding how the ontologies are intended to be used, but it seems to me that component terms should try to avoid phylogenetic specification wherever possible, unless one wants to put the prokaryotic/eukaryotic split all the way up at the top. Otherwise, making the division for things like ribosomes can be done at too many different levels, and three vs four rRNA splits would make more sense above cytosolic vs organellar so that eukaryotic organellar would be lumped with eubacterial and archaeal, and eukaryotic cytosolic would be the outgroup. That strikes me as contrary to the "understanding the unity of life" aspect of using GO. --JimHu 21:42, 22 November 2007 (PST)

NADH and reaction centre

NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)
NADH dehydrogenase complex (quinone) (sensu Bacteria)
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria)


People:

Michelle
Jim Hu


Questions:

Plan:



somitomeric trunk muscle development (sensu Mammalia)

People:

David
Victoria
Emily


Questions:

Plan:

Probably merge with parent.


reaction center (sensu ProteoBacteria)

People:


Jim Hu
Michelle
Jen

Questions:

Plan:

Debby Siegele (Texas A&M) speaking: Reaction center (sensu ProteoBacteria) is one of three child terms for GO:0009521: photosystem. The definitions of the other two child terms (GO:0009522: photosystem I and GO:009523: photosystem II) are specific for plants and cyanobacteria (the prokaryotic group that includes the ancestor of plant and algal chloroplasts). This is probably what led to the creation of a child term specific for the photosynthetic Proteobacteria. In addition to the two groups of photosynthetic purple bacteria that belong to the phylum Protebacteria, there are also three other groups of photosynthetic bacteria: the green sulfur bacteria, the green filamentous bacteria, and the heliobacteria.

In literature that includes all types of photosynthesis reaction centers, the two types of photosystems are defined in a more inclusive way according to the nature of the electron acceptors. For example, see the following from Allen and Williams, FEBS Lett. 1998. Photosynthetic reaction centers. 438(1-2):5-9. (PMID:9821949).

"Photosynthetic reaction centers can be classed into two categories based upon the nature of the electron acceptors (for a review see [R.E. Blankenship. Photosynth. Res. 33 (1992), pp. 91–111]. Purple bacteria, green filamentous bacteria, and photosystem II belong to the pheophytin-quinone type, while green sulfur bacteria, heliobacteria, and photosystem I belong to the iron-sulfur type (Fig. 1). While anoxygenic bacteria have only one photosystem, cyanobacteria and plants contain both types of photosystems. A structure for each type of reaction center has been determined by X-ray diffraction, and generalizations can be drawn from these structures since sequence comparisons indicate that all the reaction centers within each type are homologous (emphasis added)."

Redefining the GO terms for photosystems I and II would allow term GO:0030090: reaction center (sensu ProteoBacteria) to be eliminated. New definitions would also illustrate the homology within each type of photosystem. Photosystems I and II both have child terms. My initial view is that that redefining the parent terms will not affect whether the child terms still follow the "true path rule", but this needs to be looked at more carefully.


Finished Work