Difference between revisions of "Meeting Notes 3"

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==spores and cell walls==
[[Category:GO Consortium Meetings]]
==Electron transport==


spore wall assembly (sensu Bacteria) <br>
[http://wiki.geneontology.org/index.php/Electron_transport Electron transport]
spore wall assembly (sensu Fungi) <br>
spore wall (sensu Fungi) <br>


sporulation (sensu Bacteria) <br>
sporulation (sensu Fungi) <br>
spore development (sensu Magnoliophyta) <br>


'''People:'''<br>
==sporulation==
Moved to [[Sporulation Meeting Notes]]


Val<br>
==proteasome==
Maria Costanzo<br>
Michelle<br>
Midori<br>
Pascale<br>
Jen<br>
Jim Hu<br>
Tanya<br>
 
'''Questions:'''<br>
 
What are the distinguishing features of the walls?<br>
or
What are the distinguishing features of the assembly of the walls?<br>
Ask Chris Brett if he knows difference between plant, bacterial, and fungal cell walls. <br>
Also relevant to cell walls. [Jen]
 
 
'''Plan:'''<br>
 
'''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:''' The introduction in this publication - PMID:15590821 - has a nice description of what is unique about S. cerevisiae spores.
 
 
'''Notes/action items from Skype Webex meeting/ Midori/Val & Maria Fi 2nd Nov'''
 
1. chitin and beta glucan containing cell wall
We needed to get rid of chitin and beta-glucan containing cell wall as that does not work for pombe.
(pombe cell walls don't have chitin , although spores do).
 
Propose solution:
Change term name to "fungal-type cell wall".
 
This needs to be defined based on features which distinguish the fungal cell wall, but the def can be refined/clarified to include remarks on features that this type of cell wall does not have (cellulose/pectin) to distinguish from non-fungal cell walls.
 
Maria: Here's a proposed definition for "fungal-type cell wall", based on the current one for 'chitin and beta-glucan containing cell wall' but hopefully broadened to include all fungi:
 
A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis, consisting of extensively cross-linked glycoproteins and carbohydrates. The glycoproteins may be modified with N- or O-linked carbohydrates, or glycosylphosphatidylinositol (GPI) anchors; the polysaccharides are primarily branched glucans, including beta-linked and alpha-linked glucans, and may also include chitin and other carbohydrate polymers, but not cellulose or pectin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure.
 
Current dbxrefs:[source: GOC:mtg_sensu_feb07, ISBN:3540601864, PMID:11283274, PMID:3319422] and we should add PMID:16927300.
 
2. Spore wall
 
Similarly change term 'spore wall (sensu fungi)' to 'fungal spore wall' (fungal-type spore wall?)
 
Val to write new def which distinguishes fungal spores from bacterial spores (i.e. include something about being a product of meiosis)
 
(N.B. There currently is not a term for plant spores. if it turns out that this term is not appropriate for plant spores they can raise a new term later, if required)
 
3. invasive growth (sensu fungi) (see below)
 
4. yeast-form cell wall
 
Maria to refine def to include 'budding'
 
Maria: Here's a draft:
The wall surrounding a cell of a dimorphic fungus growing in the single-cell budding yeast form, in contrast to the filamentous or hyphal form.
 
 
'''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.
 
==neural rod==
 
neural rod cavitation (sensu Teleost) <br>
neural rod formation (sensu Teleost) <br>


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


Also see [https://sourceforge.net/tracker/index.php?func=detail&aid=1848103&group_id=36855&atid=440764| SF 1848103]
'''People:'''<br>
'''People:'''<br>


Doug<br>
Rama<br>
David<br>
Jim Hu<br>
Michelle<br>
Kate Dreher (TAIR)<br>
Tanya <br>


'''Questions:'''<br>
'''Questions:'''<br>


How do we distinguish neural rods in Teleosts and other things. Does anything else have neural rods?
'''Comments:'''<br>
Neurulation in teleosts is a bit different than it is in other verts.  For example, many verts have a clear distinction b/t primary neurulation (epithelial folding etc..) vs. secondary neurulation (mesenchymal cavitation process).  In the case of teleosts, they form a 'neural rod' which has an epithelial origin, so is primary neurulation like, but the cell movements are slightly different.  Epithelial cells form a solid dorsal structure (the neural keel) which then morphs into a tube (the neural rod) which then cavitates to form the neural tube.  It's like primary neurulation in that it has epithelial origins, but is sort of like secondary neurulation in that it is a cavitation process rather than a folding process to form the tube.  From what I can find in the literature, the 'neural rod' refers to the developing teleost neural tube structure of epidermal origin.  Other verts that use the more conventional primary and secondary neurulation mechanism won't have this structure.  Long story short:  I think we might be able to simply drop (sensu Telost) from both of these terms.
-Doug
We might be more correct to move 'neural keel formation' to the same level as 'neural rod formation' rather than them having a  'part of' relation to each other.  The neural keel develops into the neural rod through a morphogenetic change, but perhaps they are to be considered distinct anatomical structures.
-Doug
NOTE 10/17/07:  Changes to the 'neural rod....sensu teleost' terms are waiting for pending discussion between Melissa H. and myself. 
'''Plan:'''<br>
'''Plan:'''<br>


Written to Doug to ask if he has thought further about this 13/12/07.Jen<br>
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.


12/13/07
2Drop (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.
We believe the 'neural rod' is a teleost specific structureTherefore it should be fine to drop the 'sensu telost' from the term names. The defs are fairly clear on the term meanings.
-Doug


==gastrulation==
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).


gastrulation (sensu Vertebrata) <br>
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.
gastrulation (sensu Mammalia) <br>
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.


'''People:'''<br>
6. Drop (s E) from ‘cytosolic proteasome regulatory particle (sensu Eukaryota)’  and improve definition from


David<br>
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).
Doug<br>
Victoria<br>


'''Questions:'''<br>
To


What distinguishes mammalian gastrulation from other organisms?<br>
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.


'''Plan:'''<br>
7. Drop (s E) from ‘cytosolic proteasome complex (sensu Eukaryota)‘ and improve definition from


Find distinguishing feature or merge terms. <br>
A proteasome found in the cytosol of a cell; as in, but not restricted to, the eukaryotes (Eukaryota, ncbi_taxonomy_id:2759).


To


I am tempted to merge the vertebrate term and the mammalian term into the parent and then just make part-of children that are found in gastrulation of different beasts. It turns out that all the beasts use different members of the child set, but they all use different ones. The children are:<br>
A proteasome complex found in the cytosol of a cell.
# invagination involved in gastrulation with mouth forming second is_a morphogenesis of an epithelial sheet<br>
# involution involved in gastrulation with mouth forming second is_a morphogenesis of an epithelial sheet<br>
# ingression involved in gastrulation with mouth forming second is_a cell migration involved in gastrulation<br>
# delamination involved in gastrulation with mouth forming second  is_a negative regulation of  cell-cell adhesion (we should probably have a generic delamination term)<br>
# epiboly involved in gastrulation with mouth forming second is_a morphogenesis of an epithelial sheet<br>


I'd get the defs straight from Gilbert.


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


==larval development==
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).


larval development (sensu Amphibia) <br>
To
larval development (sensu Nematoda) <br>


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


'''People:'''<br>
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).


Becky Foulger<br>
To
Kimberly<br>


'''Questions:'''<br>
Refers to the subcomplex of the proteasome regulatory particle that forms the peripheral lid, which is added on top of the base subcomplex.


What are the distinguishing features?<br>
10.  Drop (s E) from ‘proteasome core complex, alpha-subunit complex (sensu Eukaryota)’ and improve definition from
Is it worth having separate terms for each?<br>


'''Plan:'''<br>
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).


Yes, I do think we'll need to have separate terms for each.  The distinguishing features seem significantly different enough to warrant that.
To
Nematode larvae have essentially the same body plan as adults, but grow larger and develop specific anatomical structures during larval development.  Also, the successive molts at larvae stage transitions is a key component of nematode larval development.


--Kimberly
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


Shall we just make these amphibian larval development and nematode larval development? We can make really clear defs to show the differences.  
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).


--Jen
To


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


That sounds reasonable. Here is a proposed definition for nematode larval development:
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.


The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (e. g., fourth larval stage (L4) in C. elegans).  Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan.  Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew. 
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:


--Kimberly
‘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)


From Becky:
    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.


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


The process whose specific outcome is the progression of the amphibian larva over time, from its formation to the mature structure. Amphibian larvae, sometimes called pollywogs or tadpoles, hatch from eggs and begin to grow limbs and other adult physical features at various times, depending on the species, before they metamorphose into the adult form.
An obsoletions warning mail has been sent.  


Mainly taken from http://www.livingunderworld.org/biology/.


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


==proteasome==
proteasome core complex (sensu Eukaryota) <br>
cytosolic proteasome core complex (sensu Eukaryota) <br>
proteasome regulatory particle (sensu Eukaryota) <br>
cytosolic proteasome regulatory particle (sensu Eukaryota) <br>
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br>
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br>
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br>
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br>
proteasome complex (sensu Eukaryota) <br>
cytosolic proteasome complex (sensu Eukaryota) <br>
proteasome core complex (sensu Bacteria) <br>
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br>
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br>
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br>
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br>
proteasome regulatory particle (sensu Bacteria) <br><br>
Also see [https://sourceforge.net/tracker/index.php?func=detail&aid=1848103&group_id=36855&atid=440764| SF 1848103]


'''People:'''<br>
[Term]<br>
 
id: GO:0022624<br>
Rama<br>
name: proteasome accessory complex<br>
Jim Hu<br>
namespace: cellular_component<br>
Michelle<br>
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]<br>
is_a: GO:0043234 ! protein complex<br>
relationship: part_of GO:0000502 ! proteasome complex<br>
<br>
[Term]<br>
id: GO:0022625<br>
name: cytosolic large ribosomal subunit<br>
namespace: cellular_component<br>
alt_id: GO:0005842<br>
alt_id: GO:0009282<br>
alt_id: GO:0030498<br>
alt_id: GO:0030872<br>
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]<br>
synonym: "50S ribosomal subunit" NARROW []<br>
synonym: "60S ribosomal subunit" NARROW []<br>
synonym: "cytosolic large ribosomal subunit (sensu Archaea)" NARROW []<br>
synonym: "cytosolic large ribosomal subunit (sensu Bacteria)" NARROW []<br>
synonym: "cytosolic large ribosomal subunit (sensu Eukaryota)" NARROW []<br>
synonym: "eukaryotic ribosomal LSU" NARROW []<br>
synonym: "prokaryotic large ribosomal subunit" NARROW []<br>
is_a: GO:0015934 ! large ribosomal subunit<br>
is_a: GO:0044445 ! cytosolic part<br>
relationship: part_of GO:0022626 ! cytosolic ribosome<br>
<br>
[Term]<br>
id: GO:0022626<br>
name: cytosolic ribosome<br>
namespace: cellular_component<br>
alt_id: GO:0005830<br>
alt_id: GO:0009281<br>
alt_id: GO:0030871<br>
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]<br>
synonym: "70S ribosome" NARROW []<br>
synonym: "80S ribosome" NARROW []<br>
synonym: "cytosolic ribosome (sensu Archaea)" NARROW []<br>
synonym: "cytosolic ribosome (sensu Bacteria)" NARROW []<br>
synonym: "cytosolic ribosome (sensu Eukaryota)" NARROW []<br>
is_a: GO:0005840 ! ribosome<br>
is_a: GO:0044445 ! cytosolic part<br>
<br>
[Term]<br>
id: GO:0022627<br>
name: cytosolic small ribosomal subunit<br>
namespace: cellular_component<br>
alt_id: GO:0005843<br>
alt_id: GO:0009283<br>
alt_id: GO:0030499<br>
alt_id: GO:0030873<br>
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]<br>
synonym: "30S ribosomal subunit" NARROW []<br>
synonym: "40S ribosomal subunit" NARROW []<br>
synonym: "cytosolic small ribosomal subunit (sensu Archaea)" NARROW []<br>
synonym: "cytosolic small ribosomal subunit (sensu Bacteria)" NARROW []<br>
synonym: "cytosolic small ribosomal subunit (sensu Eukaryota)" NARROW []<br>
synonym: "eukaryotic ribosomal SSU" NARROW []<br>
synonym: "prokaryotic small ribosomal subunit" NARROW []<br>
is_a: GO:0015935 ! small ribosomal subunit<br>
is_a: GO:0044445 ! cytosolic part<br>
relationship: part_of GO:0022626 ! cytosolic ribosome<br>
<br>
[Term]<br>
id: GO:0022628<br>
name: chloroplast large ribosomal subunit<br>
namespace: cellular_component<br>
def: "The large subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br>
is_a: GO:0000311 ! plastid large ribosomal subunit<br>
relationship: part_of GO:0043253 ! chloroplast ribosome<br>
<br>
[Term]<br>
id: GO:0022629<br>
name: chloroplast small ribosomal subunit<br>
namespace: cellular_component<br>
def: "The small subunit of a ribosome contained within a chloroplast." [GOC:mtg_sensu]<br>
is_a: GO:0000312 ! plastid small ribosomal subunit<br>
relationship: part_of GO:0043253 ! chloroplast ribosome<br>


'''Questions:'''<br>


'''Plan:'''<br>


==cytosolic ribosome==
==cytosolic ribosome==
Line 281: Line 244:
   
   
  The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br>  
  The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br>  
  Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. These are generated from post-transcriptional processing of a single rRNA precursor.   
  Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. <br>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) <br>
  Prokaroytic ribosomes contain about 50 proteins.  The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br>
  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   
  Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are<br> 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   
  precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA <br>polymerase III, whereas the large transcript containing   
  the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in fact much larger than it's bacterial counterpart  
  the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in <br>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.<br>
  (~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt.  Eukaryotic ribosomes <br>contain 70-80 proteins.<br>
  I would think that the most single feature is the 3 vs 4 chain.<br>
  I would think that the most single feature is the 3 vs 4 chain.<br>
  Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal mitochondrial ribosomes lack 5 sRNA, and are   
  Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal <br>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).<br>
  thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then <br>you would b safe).<br>
  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  
  The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have <br>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. <br>
  expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br>
  I propose <br>
  I propose <br>
  1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br>
  1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br>
  2. Four-RNA chain containing  ribosomes. ( 5.8s-, eukarytotic-type)<br>
  2. Four-RNA chain containing  ribosomes. ( 5.8s-, eukarytotic-type)<br>
  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   
  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. <br>Although I wouldn't be adverse to using   
  &ldquo;5.8s-containing ribosome vs ??).<br>
  &ldquo;5.8s-containing ribosome vs ??).<br>
  Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.
  Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.
Line 338: Line 301:




==somitomeric trunk muscle development (sensu Mammalia) ==
'''People:'''<br>
David <br>
Victoria<br>
Emily<br>
'''Questions:'''<br>
'''Plan:'''<br>
Probably merge with parent.<br>




==plasmid partitioning (sensu Bacteria) ==
==reaction center (sensu Proteobacteria) ==




'''People:'''<br>
'''People:'''<br>


Eurie<br>
original list:<br>
Jim Hu <br>
Michelle<br>
Michelle<br>
Jen<br>
updated list:
Debby Siegele<br>
Midori<br>
Midori<br>


'''Questions:'''<br>
'''Questions:'''<br>
It seems to me that plasmid partitioning's definition applies generally to partitioning, whether it is in yeast (2 micron), mammalian cells (for dormant forms of various DNA viruses IIRC) or bacteria.  But it leads to questions
* whether the kind of host cell where the process happens is a defining property of the process.
* how granular should GO be?  There is a child term just for 2 micron - should there be whole branches for every specific plasmid?
My inclination is to fold sensu Bacteria into the parent term.
--[[User:JimHu|JimHu]] 14:21, 22 November 2007 (PST)


'''Plan:'''<br>
'''Plan:'''<br>


Eurie: I know nothing about this! =)
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.
 
 
'''Feb. 21:''' first draft  proposal (Midori; preformatted) and comments (Debby; indented)
 
<pre>
id: GO:0009521
name: photosystem
new def: A complex located in a thylakoid membrane that consists of
proteins associated with accessory pigments and electron carriers, which
operate in sequence to carry out the two light reactions of
photosynthesis. [ISBN:0140514031, PMID:9821949, GOC:mah]
</pre>
 
:Cyanobacteria are the only prokaryotes that are known to carry out both the light reactions of photosynthesis.  Other photosynthetic bacteria have only Photosystem I or Photosystem II. <br>
:Chloroplasts and cyanobacteria have thylakoid membranes, but I don't know whether other photosynthetic bacteria do.  I'll contact colleagues who work in this area and see if I can find out.
 
<pre>
id: GO:0009522
name: photosystem I
new def: A photosystem that contains an iron- sulfur reaction center and
functions as a light- dependent plastocyanin- ferredoxin oxidoreductase,
transferring electrons from plastocyanin to ferredoxin. [ISBN:0943088399,
PMID:9821949, GOC:mah]
new synonym: iron- sulfur type photosystem EXACT
</pre>
 
:I don't think that all organisms with photosystem I use plastocyanin as an electron carrier. I will look into this further.
 
<pre>
id: GO:0009523
name: photosystem II
new def: A photosystem that contains a pheophytin- quinone reaction center
and functions in the presence of light as a water- plastoquinone
oxidoreductase, transferring electrons from water to plastoquinone.
[ISBN:0943088399, PMID:9821949, GOC:mah]
new synonym: pheophytin- quinone type photosystem EXACT
</pre>


==somitomeric trunk muscle development (sensu Mammalia) ==
:Not all organisms with Photosystem II oxidize water.  Only cyanobacteria  do oxygenic photosynthesis, none of the other photosynthetic bacteria do (they perform  nonoxygenic photosynthesis).<br>
:Some photosynthetic bacteria use different quinones as an electron carrier, not just plastoquinone.




'''People:'''<br>
'''April 1:''' More comments, and new proposed definitions, from Debby


David <br>
In AmiGO, photosystems are under GO:0043229 (intracellular organelle) and GO:0009579
Victoria<br>
(thylakoid).
Emily<br>


* In bacteria, the photosystems are not contained in an intracellular organelle. In some photosynthetic bacteria, the photosystems are clustered in the plasma membrane. In other photosynthetic bacteria, the plasma membrane invaginates and forms a thylakoid-like structure, but it is still a continuation of the plasma membrane.


'''Questions:'''<br>
* Colleagues who work on photosynthesis say that "thylakoid" is a particular type of photosynthetic membrane, specifically the photosynthetic membranes found in chloroplasts and cyanobacteria. The term thylakoid isn't usually used for the photosynthetic membranes found in other organisms.


'''Plan:'''<br>


Probably merge with parent.<br>
id: GO:0009521<br>
name: photosystem<br>
new def: A complex located in a thylakoid membrane that consists of proteins associated with
accessory pigments and electron carriers, which operate in sequence to carry out the two light
reactions of photosynthesis. [ISBN:0140514031, PMID:9821949, GOC:mah]


==invasive growth (sensu Saccharomyces) ==
*Only cyanobacteria and chloroplasts have both photosystem I and photosystem II, so these are the only organisms where the photosystems "operate in sequence to carry out the two light reactions of photosynthesis." Also, as I wrote above, thylakoid refers specifically to the photosynthetic membranes of cyanobacteria and chloroplasts.


*Suggested definition: A membrane-bound complex that consists of a photoreaction center associated with accessory pigments and electron carriers.


'''People:'''<br>


Maria Costanzo<br>
id: GO:0009522<br>
Val<br>
name: photosystem I<br>
new def: A photosystem that contains an iron-sulfur reaction center and functions as a
light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin
to ferredoxin. [ISBN:0943088399, PMID:9821949, GOC:mah]<br>
new synonym: iron-sulfur type photosystem EXACT


*This definition is specific for cyanobacteria and chloroplasts. The bacteria that have only a single type I photosystem, such as the green sulfur bacteria, the electrons don't come from plastocyanin and don't also go to ferredoxin. I've attached a figure from Prescott's Microbiology 6th ed. The figure shows that there's a fork at the FeS protein, where electrons can go either to ferredoxin (Fd) -> NAD+ or to menaquinone (MK) -> Cytb/FeS -> Cytc555 -> photosystem I (cyclic photophosphorylation). When electrons are transferred to Fd -> NAD+, the photoreaction center is re-reduced by electrons from thiosulfate and H2S.


'''Questions:'''<br>
*Suggested definition: A photosystem that contains an iron-sulfur reaction center associated with accessory pigments and electron carriers.


https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1583546&group_id=36855 <br>
Also consider pseudohyphal growth and filamentous growth.<br>


'''Plan''' (from Nov. 2 meeting): rename to 'fungal-type invasive growth'; make sure mention of budding pattern in def is worded so it's not too restrictive (i.e. so pombe can also use the term); otherwise, the def is good as is.<br>
id: GO:0009522<br>
name: photosystem I<br>
new def: A photosystem that contains an iron-sulfur reaction center and functions as a
light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin
to ferredoxin. [ISBN:0943088399, PMID:9821949, GOC:mah]<br>
new synonym: iron-sulfur type photosystem EXACT


*On looking at this again, I have a couple thoughts:
*This definition is specific for cyanobacteria and chloroplasts. The bacteria that have only a single type I photosystem, such as the green sulfur bacteria, the electrons don't come from plastocyanin and don't also go to ferredoxin. I've attached a figure from Prescott's Microbiology 6th ed. The figure shows that there's a fork at the FeS protein, where electrons can go either to ferredoxin (Fd) -> NAD+ or to menaquinone (MK) -> Cytb/FeS -> Cytc555 -> photosystem I (cyclic photophosphorylation). When electrons are transferred to Fd -> NAD+, the photoreaction center is re-reduced by electrons from thiosulfate and H2S.
**this term, as well as 'pseudohyphal growth', have parentage under both 'cell growth' and 'growth'. I would argue that the 'cell growth' parentage should be removed since these are multicellular phenomena.
**I don't think the 'fungal-type invasive growth' term name is very clear, since severl different kinds of filamentous growth can result in invasion of the medium. How about renaming it 'filamentous growth in response to glucose limitation'? Would pombe be able to use the 'hyphal growth' term?


==reaction center (sensu ProteoBacteria) ==
*Suggested definition: A photosystem that contains an iron-sulfur reaction center associated with accessory pigments and electron carriers.




'''People:'''<br>
id: GO:0009523<br>
name: photosystem II <br>
new def: A photosystem that contains a pheophytin- quinone reaction center and functions in
the presence of light as a water- plastoquinone oxidoreductase, transferring electrons from
water to plastoquinone. [ISBN:0943088399, PMID:9821949, GOC:mah] <br>
new synonym: pheophytin- quinone type photosystem EXACT


*Only cyanobacteria and chloroplasts oxidize water to O2 (oxygenic photosynthesis). The other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center. For example, the purple sulfur bacteria use S compounds as the source of electrons; the purple nonsulfur bacteria use organic compounds, such as succinate.


Jim Hu <br>
*Suggested definition: A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers.
Michelle<br>
Jen<br>


'''Questions:'''<br>


'''Plan:'''<br>
'''April 2:''' Additions to Debby's draft (Midori)


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.
*Add to new reaction center defs to indicate that the complexes are located in photosynthetic membranes.


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).
*Reorganization around thylakoid terms to accommodate non-thylakoid photosynthetic membranes
**add a new term, "photosynthetic membrane", as an is_a child of membrane
**move thylakoid to be an is_a child of the new term
**copy chloroplast thylakoid back to is_a membrane-bounded organelle
**move the photosystem terms to be children of the new term (also add a term for "photosynthetic membrane part" for the sake of is_a completeness)


"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.
'''April 3: DONE!'''




[[Finished Work]]
[[Finished Work]]

Latest revision as of 18:48, 23 April 2014

Electron transport

Electron transport


sporulation

Moved to Sporulation Meeting Notes

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:

original list:
Jim Hu
Michelle
Jen

updated list: Debby Siegele
Midori

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.


Feb. 21: first draft proposal (Midori; preformatted) and comments (Debby; indented)

id: GO:0009521
name: photosystem
new def: A complex located in a thylakoid membrane that consists of 
proteins associated with accessory pigments and electron carriers, which 
operate in sequence to carry out the two light reactions of 
photosynthesis. [ISBN:0140514031, PMID:9821949, GOC:mah]
Cyanobacteria are the only prokaryotes that are known to carry out both the light reactions of photosynthesis. Other photosynthetic bacteria have only Photosystem I or Photosystem II.
Chloroplasts and cyanobacteria have thylakoid membranes, but I don't know whether other photosynthetic bacteria do. I'll contact colleagues who work in this area and see if I can find out.
id: GO:0009522
name: photosystem I
new def: A photosystem that contains an iron- sulfur reaction center and 
functions as a light- dependent plastocyanin- ferredoxin oxidoreductase, 
transferring electrons from plastocyanin to ferredoxin. [ISBN:0943088399, 
PMID:9821949, GOC:mah]
new synonym: iron- sulfur type photosystem EXACT
I don't think that all organisms with photosystem I use plastocyanin as an electron carrier. I will look into this further.
id: GO:0009523
name: photosystem II
new def: A photosystem that contains a pheophytin- quinone reaction center 
and functions in the presence of light as a water- plastoquinone 
oxidoreductase, transferring electrons from water to plastoquinone. 
[ISBN:0943088399, PMID:9821949, GOC:mah]
new synonym: pheophytin- quinone type photosystem EXACT
Not all organisms with Photosystem II oxidize water. Only cyanobacteria do oxygenic photosynthesis, none of the other photosynthetic bacteria do (they perform nonoxygenic photosynthesis).
Some photosynthetic bacteria use different quinones as an electron carrier, not just plastoquinone.


April 1: More comments, and new proposed definitions, from Debby

In AmiGO, photosystems are under GO:0043229 (intracellular organelle) and GO:0009579 (thylakoid).

  • In bacteria, the photosystems are not contained in an intracellular organelle. In some photosynthetic bacteria, the photosystems are clustered in the plasma membrane. In other photosynthetic bacteria, the plasma membrane invaginates and forms a thylakoid-like structure, but it is still a continuation of the plasma membrane.
  • Colleagues who work on photosynthesis say that "thylakoid" is a particular type of photosynthetic membrane, specifically the photosynthetic membranes found in chloroplasts and cyanobacteria. The term thylakoid isn't usually used for the photosynthetic membranes found in other organisms.


id: GO:0009521
name: photosystem
new def: A complex located in a thylakoid membrane that consists of proteins associated with accessory pigments and electron carriers, which operate in sequence to carry out the two light reactions of photosynthesis. [ISBN:0140514031, PMID:9821949, GOC:mah]

  • Only cyanobacteria and chloroplasts have both photosystem I and photosystem II, so these are the only organisms where the photosystems "operate in sequence to carry out the two light reactions of photosynthesis." Also, as I wrote above, thylakoid refers specifically to the photosynthetic membranes of cyanobacteria and chloroplasts.
  • Suggested definition: A membrane-bound complex that consists of a photoreaction center associated with accessory pigments and electron carriers.


id: GO:0009522
name: photosystem I
new def: A photosystem that contains an iron-sulfur reaction center and functions as a light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin to ferredoxin. [ISBN:0943088399, PMID:9821949, GOC:mah]
new synonym: iron-sulfur type photosystem EXACT

  • This definition is specific for cyanobacteria and chloroplasts. The bacteria that have only a single type I photosystem, such as the green sulfur bacteria, the electrons don't come from plastocyanin and don't also go to ferredoxin. I've attached a figure from Prescott's Microbiology 6th ed. The figure shows that there's a fork at the FeS protein, where electrons can go either to ferredoxin (Fd) -> NAD+ or to menaquinone (MK) -> Cytb/FeS -> Cytc555 -> photosystem I (cyclic photophosphorylation). When electrons are transferred to Fd -> NAD+, the photoreaction center is re-reduced by electrons from thiosulfate and H2S.
  • Suggested definition: A photosystem that contains an iron-sulfur reaction center associated with accessory pigments and electron carriers.


id: GO:0009522
name: photosystem I
new def: A photosystem that contains an iron-sulfur reaction center and functions as a light-dependent plastocyanin-ferredoxin oxidoreductase, transferring electrons from plastocyanin to ferredoxin. [ISBN:0943088399, PMID:9821949, GOC:mah]
new synonym: iron-sulfur type photosystem EXACT

  • This definition is specific for cyanobacteria and chloroplasts. The bacteria that have only a single type I photosystem, such as the green sulfur bacteria, the electrons don't come from plastocyanin and don't also go to ferredoxin. I've attached a figure from Prescott's Microbiology 6th ed. The figure shows that there's a fork at the FeS protein, where electrons can go either to ferredoxin (Fd) -> NAD+ or to menaquinone (MK) -> Cytb/FeS -> Cytc555 -> photosystem I (cyclic photophosphorylation). When electrons are transferred to Fd -> NAD+, the photoreaction center is re-reduced by electrons from thiosulfate and H2S.
  • Suggested definition: A photosystem that contains an iron-sulfur reaction center associated with accessory pigments and electron carriers.


id: GO:0009523
name: photosystem II
new def: A photosystem that contains a pheophytin- quinone reaction center and functions in the presence of light as a water- plastoquinone oxidoreductase, transferring electrons from water to plastoquinone. [ISBN:0943088399, PMID:9821949, GOC:mah]
new synonym: pheophytin- quinone type photosystem EXACT

  • Only cyanobacteria and chloroplasts oxidize water to O2 (oxygenic photosynthesis). The other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center. For example, the purple sulfur bacteria use S compounds as the source of electrons; the purple nonsulfur bacteria use organic compounds, such as succinate.
  • Suggested definition: A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers.


April 2: Additions to Debby's draft (Midori)

  • Add to new reaction center defs to indicate that the complexes are located in photosynthetic membranes.
  • Reorganization around thylakoid terms to accommodate non-thylakoid photosynthetic membranes
    • add a new term, "photosynthetic membrane", as an is_a child of membrane
    • move thylakoid to be an is_a child of the new term
    • copy chloroplast thylakoid back to is_a membrane-bounded organelle
    • move the photosystem terms to be children of the new term (also add a term for "photosynthetic membrane part" for the sake of is_a completeness)


April 3: DONE!


Finished Work