Closed gocentral closed 9 years ago
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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
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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
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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
Original comment by: brendamg
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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
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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
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Added new term 'periplsmic space ; GO:0042597' synonym:periplasm as child of cell.
Original comment by: jl242
Original comment by: jl242
Original comment by: jl242
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