Difference between revisions of "Meeting Notes 3"

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Debby Siegele (Texas A&M) speaking:  This 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.   
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).
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).

Revision as of 14:58, 25 November 2007

spores and cell walls

spore wall assembly (sensu Bacteria)
spore wall assembly (sensu Fungi)
spore wall (sensu Fungi)

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

People:

Val
Maria Costanzo
Michelle
Midori
Pascale
Jen
Jim Hu
Tanya

Questions:

What are the distinguishing features of the walls?
or What are the distinguishing features of the assembly of the walls?
Ask Chris Brett if he knows difference between plant, bacterial, and fungal cell walls.
Also relevant to cell walls. [Jen]


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: 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)
neural rod formation (sensu Teleost)


People:

Doug
David

Questions:

How do we distinguish neural rods in Teleosts and other things. Does anything else have neural rods?

Comments:

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:

gastrulation

gastrulation (sensu Vertebrata)
gastrulation (sensu Mammalia)


People:

David
Doug
Victoria

Questions:

What distinguishes mammalian gastrulation from other organisms?

Plan:

Find distinguishing feature or merge terms.


larval development

larval development (sensu Amphibia)
larval development (sensu Nematoda)


People:

Becky Foulger
Kimberly

Questions:

What are the distinguishing features?
Is it worth having separate terms for each?

Plan:

Yes, I do think we'll need to have separate terms for each. The distinguishing features seem significantly different enough to warrant that. 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


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

--Jen

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)


People:

Rama
Jim Hu
Michelle

Questions:

Plan:



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:




plasmid partitioning (sensu Bacteria)

People:

Eurie
Michelle
Midori


Questions:
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. --JimHu 14:21, 22 November 2007 (PST)

Plan:

Eurie: I know nothing about this! =)

somitomeric trunk muscle development (sensu Mammalia)

People:

David
Victoria
Emily


Questions:

Plan:

Probably merge with parent.

otolith

otolith mineralization (sensu Actinopterygii)
otolith mineralization (sensu Tetrapoda)


People:

David Fashena
https://sourceforge.net/tracker/index.php?func=detail&aid=1109256&group_id=36855&atid=440764
Midori
David
Emily
Victoria
Doug (I can consult with Dave F. as he is in the next office over)

Questions:

Comments:

I believe the initial introduction of the 'sensu Actinopterygii' term was because fish otoliths continue to grow throughout the life of the fish. It was my understanding that this was not true for tetrapods. If this distinction doesn't hold water, then perhaps a merge could happen.

-Doug

I have written to the GO list to see if anyone knows. 20 Nov 2007.


Plan:

outer membrane biogenesis (sensu ProteoBacteria)

People:

Jim Hu
Michelle


Questions:

Check how we distinguish the outer membrane in the component ontology.


Plan:
It looks like the sensu terms have already been addressed in the component ontology. Shouldn't the biogenesis process term point to the component term? If this is mirrored in the biogenesis term, then it seems to me that the sensu should be removed from the biogenesis term and GO:0043165 outer membrane biogenesis (sensu ProteoBacteria) should be renamed to GO:0043165 cell outer membrane biogenesis and the definition should be

The assembly of a cell outer membrane [GO: 0009279]. As in, but not restricted to, the Gram-negative bacteria

Looking at these raises some other issues that we will put on Sourceforge. --JimHu 14:38, 22 November 2007 (PST)

invasive growth (sensu Saccharomyces)

People:

Maria Costanzo
Val


Questions:

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

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.

  • On looking at this again, I have a couple thoughts:
    • 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)

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."

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