periplasm=periplasmic space; keep obsolete term GO:0005620

[gocentral]

I would suggest the term periplasm as a synonym term for periplasmic space.

<periplasmic space (sensu Fungi) ; GO:0030287 ; synonym:periplasm (sensu Fungi) <periplasmic space (sensu Gram-negative Bacteria) ; GO:0030288; synonym:periplasm (sensu Gram-negative Bacteria)

Further I would suggest to add a term <periplasmic space (sensu Viridiplantae) ; GO:00nnnn ; synonym:periplasm (sensu Viridiplantae)

Cheers, Marion

Reported by: brendamg

Original Ticket: "geneontology/ontology-requests/635":https://sourceforge.net/p/geneontology/ontology-requests/635

[gocentral]

Logged In: YES user_id=679735

Furthermore I would prefer to keep %periplasmic space ; GO:0005620 as an umbrella term.

Cp.:
%cell wall ; GO:0005618 %cell wall (sensu Bacteria) ; GO:0009274 ; %cell wall (sensu Gram-negative Bacteria) ; GO:0009276 ; %cell wall (sensu Gram-positive Bacteria) ; GO:0009275 ; %cell wall (sensu Fungi) ; GO:0009277

Cp.: <flagellum ; GO:0019861 %flagellum (sensu Bacteria) ; GO:0009288 %flagellum (sensu Eukarya) ; GO:0009434

Original comment by: brendamg

[gocentral]

Logged In: YES user_id=579762

I don't think there is a periplasm / periplasmic space in plant cells, at least not as it's defined for bacteria and fungi (space between plasma membrane/cell membrane and cell wall).
You might be able to use the terms apoplast or symplast to annotate the gene you are working on. See Sourceforge entry 668408 Apoplast for definitions. Do you have some literature citation that talks about periplasm in plant cells? I've looked into this a little bit and it seems that the thylakoid lumen (part of the chloroplast) might be functionally similar to the bacterial periplasm in that the protein transport/export machinery functions similarly in both systems.

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=679735

Hi Tanya,

the only reference I found is the following one:

http://www.botanik.uni-bonn.de/menzel/edelmann\_e.htm: The mechanism of the regulation of expansion growth of plant cells is still unknown. Auxin (IAA)- and gibberellin (GA)-induced elongation growth is characterized by the induced occurrence of osmiophilic particles (OPs) within the periplasmic space of the growth-controlling outer epidermal cells of plant organs.

The periplasm in Hordeum vulgare in our database was unfortunately a mistake.

But do you also think that periplasm and periplasmic space are synonym terms?

It is more important for us to keep the term %periplasmic space ; GO:0005620 as an umbrella term. Our dataset writer shouldn`t decide wether a term is "sensu Fungi" or "sensu Gram-negative Bacteria".

Cheers, Marion

Original comment by: brendamg

[gocentral]

• summary: periplasm=periplasmic space & ps (sensu Viridiplantae) --> periplasm=periplasmic space; keep obsolete term GO:0005620

Original comment by: brendamg

[gocentral]

Logged In: YES user_id=579762

Hi Marion,

I do think that periplasm and periplasmic space are synonyms. See this definition from the Oxford Dictionary of Biology: periplasm (periplasmic space)
The zone between the cytoplasmic membrane and the outer membrane in Gram-negative bacteria. It contains a thin layer of peptidoglycan, has a gel-like consistency, and contains various types of proteins concerned with the cell's metabolism.

I'm guessing that yeast have similar structures or else the sensu Fungi term wouldn't exist. I think that if the umbrella term can be defined appropriately, it should be reinstated. It appears to me that it was obsoleted due to incorrect definition and users were referred to the two child terms.

As for the use of 'periplasmic space/periplasm' for plants, I think the case you found was unusual and is not the norm. I would prefer if we did not create a term like this in the GO.
Let me know if you have trouble assigning your genes to another, more appropriate term.

Cheers,

Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=451873

So:

---%periplsmic space ; GO:new synonym:periplasm ------%periplasmic space (sensu Gram-negative Bacteria) ; GO:0030288 ------%periplasmic space (sensu Fungi) ; GO:0030287

Definition: The region outside the cell plasma membrane and within the cell wall or outer membrane.

The question is where to put the generic term - at the moment periplasmic space (sensu Fungi) is part_of cell wall (sensu Fungi) while periplasmic space (sensu Gram-negative Bacteria) is part_of cell envelope.

One way to do it would be to put the generic 'periplasmic space' directly under 'external encapsulating structure'. The 'periplasmic space (sensu Fungi)' could then be moved from being part_of 'cell wall (sensu Fungi)' to be a child of this term (because isn't really part of the cell wall as such):

external encapsulating structure ---%cell envelope ------<cell wall (sensu Gram-negative Bacteria) ------<external outer membrane (sensu Gram-negative Bacteria) ------<periplasmic space (sensu Gram-negative Bacteria) ---%periplasmic space ------%periplasmic space (sensu Gram-negative Bacteria) ------%periplasmic space (sensu Fungi)

The only problem with this is that 'periplasmic space (sensu Fungi)' isn't now part_of anything - if Fungi had something called 'cell envelope' analogous to bacteria life would be a lot easier!

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Added new term 'periplsmic space ; GO:0042597' synonym:periplasm as child of cell.

Original comment by: jl242

[gocentral]

• milestone: --> MGI
• assigned_to: nobody --> jl242

Original comment by: jl242

[gocentral]

• status: open --> closed

Original comment by: jl242