Meeting Notes 3

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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