[Ontology-editors] thylakoid membrane thread
Midori Harris
midori at ebi.ac.uk
Thu Dec 11 08:52:47 PST 2008
This is probably the email thread for
http://wiki.geneontology.org/index.php/Notes_for_cc_xp_self
---------- Forwarded message ----------
Date: Fri, 25 Jul 2008 15:43:24 +0100 (BST)
From: Midori Harris <midori at ebi.ac.uk>
To: Jim Hu <jimhu at tamu.edu>, Deborah Siegele <siegele at mail.bio.tamu.edu>,
Michelle Gwinn Giglio <mgiglio at som.umaryland.edu>,
Tanya Berardini <tberardi at acoma.stanford.edu>,
Donghui Li <donghui at stanford.edu>,
"Jennifer Deegan (nee Clark)" <jdeegan at ebi.ac.uk>
Cc: Chris Mungall <cjm at fruitfly.org>
Subject: thylakoid membrane question
Hi,
Chris and I need some assistance from someone who knows about thylakoids,
especially in prokaryotes. Chris asks (as part of SF 2019054; link below):
[Should we add this relationship?]
? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
"cytoplasmic vesicle membrane" [GO:0030659]
This inference would be true if the def of PMDTM was "a M that
sourrounds a PMDT". This would seem to be
suggested by the text def:
The pigmented membrane of a plasma membrane-derived thylakoid."
However, the DAG structure suggests that the genus of the definition
should be a *portion* of the plasma membrane that....
The use of derivation is confusing. Do we just need to use
derives_from in GO?
> From what I've gathered from GO definitions and the wiki, some bacterial
thylakoids are continuous with the plasma membrane (i.e. a portion of the
plasma membrane). As a result, the GO structure and defs are kind of confused
-- see the SF comments for more details, and let me know if you have any
questions about our questions ...
SF link:
https://sourceforge.net/tracker/index.php?func=detail&aid=2019054&group_id=36855&atid=440764
wiki page noted above:
http://wiki.geneontology.org/index.php/Meeting_Notes_3
Thanks,
Midori
---------- Forwarded message ----------
Date: Mon, 4 Aug 2008 13:03:28 +0100 (BST)
From: Midori Harris <midori at ebi.ac.uk>
To: Deborah Siegele <siegele at mail.bio.tamu.edu>
Cc: tberardi at acoma.stanford.edu, jdeegan at ebi.ac.uk, mgiglio at som.umaryland.edu,
donghui at stanford.edu, jimhu at tamu.edu, cjm at fruitfly.org
Subject: Re: thylakoid membrane question
Hi Debby,
Thanks for your very informative reply, and sorry I haven't got back to it
until now. From your mail, the GO structure, and some things I've found online,
I think we should have three terms for photosynthetic membrane structures:
- one for thylakoids in plants; 'plastid thylakoid' covers this
- one for thylakoids in cyanobacteria
- one for the photosynthetic membranes in other photosynthetic bacteria
The first two would be grouped under thylakoid (GO:0009579; I've edited the def
as you recommended). The second two can be grouped under a term for plasma
membrane-derived photosynthetic membrane -- assuming that's biologically
accurate. If not, they don't need to be grouped, and the cyanobacterial
thylakoid term can have just one parent.
In any case, all three would be descendants of the most general term,
'photosynthetic membrane' (GO:0034357).
Despite the definition wording, I think -- based on the term name and parents
-- that GO:0030075 may have been originally intended to represent
cyanobacterial thylakoids. But I also suspect that we didn't fully appreciate
that the other photosynthetic bacteria have such different photosynthetic
membrane structures, whence the muddied specificity of the definition and
parents (it was done by me and a former TAIR curator -- neither of us experts
on bacteria!).
It might be safest to use GO:0030075 as the broader 'plasma membrane-derived
photosynthetic membrane' because of the def/name inconsistency. But if we do
that, would there be any difference between GO:0030075 and 'chromatophore'
(GO:0042716, defined as "A pigment bearing structure found in certain
photosynthetic bacteria and cyanobacteria which is derived from the cytoplasmic
membrane, sometimes consisting of simple invaginations and sometimes a complete
vesicle.")? If not, they can be merged. The other option is to dclare it to be
the term for cyanobacterial thylakoids, and rephrase the definition
accordingly. Any preference?
No matter what we do with this term, we can remove the broad synonym 'thylakoid
(sensu Bacteria)' because it's a bit misleading; I'll also edit the comment on
the obsolete term 'thylakoid (sensu Bacteria)'. We can also move
'chromatophore' from under 'vesicle', since that would fit with both the
existing definition and your comments. Can it go under 'plasma membrane-derived
photosynthetic membrane'?
Thanks again,
Midori
On Thu, 31 Jul 2008, Deborah Siegele wrote:
> Hi Midori,
>
>> From scanning the literature and talking with colleagues who work on
>> photosynthesis, I think that the term thylakoid is used almost exclusively
>> for the photosynthetic membranes found in chloroplasts and in cyanobacteria.
>> Personally, I find it confusing that the word "thylakoid" is being used for
>> all photosynthetic organisms. I think of a thylakoid as the stacked
>> photosynthetic membranes that are characteristic of chloroplasts and
>> cyanobacteria.
>
> I think I would modify the first sentence of the definition of GO:0009579
> thylakoid to read: " A membraneous cellular structure that bears the
> photosynthetic pigments in plants, algae, and cyanobacteria." Another
> reason for grouping these together is that chloroplasts are generally
> accepted to have evolved from an ancestral cyanobacterial endosymbiont.
>
> Could GO:0030075 plasma membrane-derived thylakoid be renamed? Plasma
> membrane-derived photosynthetic membrane is redundant, but that is all I can
> think of right now. What sorts of structures are supposed to be annotated to
> this term? that might help in naming it.
>
> I think the definition and synonyms for GO:0030075 also need to be modified.
> The current definition is: "A membraneous cellular structure derived from,
> but not necessarily continuous with, the plasma membrane. It bears the
> photosynthetic pigments in photosynthetic bacteria." I would change it to "A
> membraneous cellular structure bearing the photosynthetic apparatus that is
> derived from, but not necessarily continuous with, the plasma membrane of
> prokaryotic cells."
>
>
> [Should we add this relationship?]
> ? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
> "cytoplasmic vesicle membrane" [GO:0030659]
>
> I'm not sure that this relationship should be added,because I'm not sure that
> the word vesicle would be used to describe all the membraneous cellular
> structures bearing the photosynthetic apparatus that are found in
> photosynthetic prokaryotes. For example, I've attached a jpg file of a
> diagram of a Chlorobium tepidum cell. The picture was taken from
> <http://kchf-45.karlov.mff.cuni.cz/~jakub/chlorosome.htm>. I wouldn't call
> this structure a vesicle, but maybe my mental image of a vesicle is too
> restricted.
>
> Regards,
>
> Debby
>
>
>
>
>
>>>> Midori Harris <midori at ebi.ac.uk> 07/25/08 9:43 AM >>>
> Hi,
>
> Chris and I need some assistance from someone who knows about thylakoids,
> especially in prokaryotes. Chris asks (as part of SF 2019054; link below):
>
> [Should we add this relationship?]
> ? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
> "cytoplasmic vesicle membrane" [GO:0030659]
> This inference would be true if the def of PMDTM was "a M that
> sourrounds a PMDT". This would seem to be
> suggested by the text def:
> The pigmented membrane of a plasma membrane-derived thylakoid."
> However, the DAG structure suggests that the genus of the definition
> should be a *portion* of the plasma membrane that....
> The use of derivation is confusing. Do we just need to use
> derives_from in GO?
>
>> From what I've gathered from GO definitions and the wiki, some bacterial
> thylakoids are continuous with the plasma membrane (i.e. a portion of the
> plasma membrane). As a result, the GO structure and defs are kind of
> confused -- see the SF comments for more details, and let me know if you
> have any questions about our questions ...
>
> SF link:
> https://sourceforge.net/tracker/index.php?func=detail&aid=2019054&group_id=36855&atid=440764
>
> wiki page noted above:
> http://wiki.geneontology.org/index.php/Meeting_Notes_3
>
> Thanks,
> Midori
>
>
---------- Forwarded message ----------
Date: Thu, 31 Jul 2008 00:24:04 -0500
From: Deborah Siegele <siegele at mail.bio.tamu.edu>
To: tberardi at acoma.stanford.edu, jdeegan at ebi.ac.uk, midori at ebi.ac.uk,
mgiglio at som.umaryland.edu, donghui at stanford.edu, jimhu at tamu.edu
Cc: cjm at fruitfly.org
Subject: Re: thylakoid membrane question
Hi Midori,
>From scanning the literature and talking with colleagues who work on photosynthesis, I think that the term thylakoid is used almost exclusively for the photosynthetic membranes found in chloroplasts and in cyanobacteria. Personally, I find it confusing that the word "thylakoid" is being used for all photosynthetic organisms. I think of a thylakoid as the stacked photosynthetic membranes that are characteristic of chloroplasts and cyanobacteria.
I think I would modify the first sentence of the definition of GO:0009579 thylakoid to read: " A membraneous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria." Another reason for grouping these together is that chloroplasts are generally accepted to have evolved from an ancestral cyanobacterial endosymbiont.
Could GO:0030075 plasma membrane-derived thylakoid be renamed? Plasma membrane-derived photosynthetic membrane is redundant, but that is all I can think of right now. What sorts of structures are supposed to be annotated to this term? that might help in naming it.
I think the definition and synonyms for GO:0030075 also need to be modified. The current definition is: "A membraneous cellular structure derived from, but not necessarily continuous with, the plasma membrane. It bears the photosynthetic pigments in photosynthetic bacteria." I would change it to "A membraneous cellular structure bearing the photosynthetic apparatus that is derived from, but not necessarily continuous with, the plasma membrane of prokaryotic cells."
[Should we add this relationship?]
? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
"cytoplasmic vesicle membrane" [GO:0030659]
I'm not sure that this relationship should be added,because I'm not sure that the word vesicle would be used to describe all the membraneous cellular structures bearing the photosynthetic apparatus that are found in photosynthetic prokaryotes. For example, I've attached a jpg file of a diagram of a Chlorobium tepidum cell. The picture was taken from <http://kchf-45.karlov.mff.cuni.cz/~jakub/chlorosome.htm>. I wouldn't call this structure a vesicle, but maybe my mental image of a vesicle is too restricted.
Regards,
Debby
>>> Midori Harris <midori at ebi.ac.uk> 07/25/08 9:43 AM >>>
Hi,
Chris and I need some assistance from someone who knows about thylakoids,
especially in prokaryotes. Chris asks (as part of SF 2019054; link below):
[Should we add this relationship?]
? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
"cytoplasmic vesicle membrane" [GO:0030659]
This inference would be true if the def of PMDTM was "a M that
sourrounds a PMDT". This would seem to be
suggested by the text def:
The pigmented membrane of a plasma membrane-derived thylakoid."
However, the DAG structure suggests that the genus of the definition
should be a *portion* of the plasma membrane that....
The use of derivation is confusing. Do we just need to use
derives_from in GO?
>From what I've gathered from GO definitions and the wiki, some bacterial
thylakoids are continuous with the plasma membrane (i.e. a portion of the
plasma membrane). As a result, the GO structure and defs are kind of
confused -- see the SF comments for more details, and let me know if you
have any questions about our questions ...
SF link:
https://sourceforge.net/tracker/index.php?func=detail&aid=2019054&group_id=36855&atid=440764
wiki page noted above:
http://wiki.geneontology.org/index.php/Meeting_Notes_3
Thanks,
Midori
---------- Forwarded message ----------
Date: Mon, 04 Aug 2008 16:21:30 -0500
From: Deborah Siegele <siegele at mail.bio.tamu.edu>
To: midori at ebi.ac.uk
Subject: Re: thylakoid membrane question
Hi Midori,
I haven't finished digesting everything you wrote, but I do have one immediate suggestion. I think that 'plasma-membrane derived photosynthetic membrane structure' might be a better name than 'plasma-membrane derived photosynthetic membrane', which is what I first suggested.
I'll contact a colleague who works on cyanobacteria and ask whether it is accurate to give thylakoids in cyanobacteria the parent of plasma-membrane derived photosynthetic membrane.
>From what I've read, I don't think there is a difference in prokaryotes between chromatophore and photosynthetic membrane. I think the distinction comes from plants, which have plastids that synthesize and store pigments but aren't photosynthetic. In the recent literature, these plastids seems to be more commonly called chromoplasts rather than chromatophores, probably to avoid confusion with "chromatophore" used to refer to pigmented cells in animals.
Regards,
Debby
>>> Midori Harris <midori at ebi.ac.uk> 08/04/08 7:03 AM >>>
Hi Debby,
Thanks for your very informative reply, and sorry I haven't got back to it
until now. From your mail, the GO structure, and some things I've found
online, I think we should have three terms for photosynthetic membrane
structures:
- one for thylakoids in plants; 'plastid thylakoid' covers this
- one for thylakoids in cyanobacteria
- one for the photosynthetic membranes in other photosynthetic bacteria
The first two would be grouped under thylakoid (GO:0009579; I've edited
the def as you recommended). The second two can be grouped under a term
for plasma membrane-derived photosynthetic membrane -- assuming that's
biologically accurate. If not, they don't need to be grouped, and the
cyanobacterial thylakoid term can have just one parent.
In any case, all three would be descendants of the most general term,
'photosynthetic membrane' (GO:0034357).
Despite the definition wording, I think -- based on the term name and
parents -- that GO:0030075 may have been originally intended to represent
cyanobacterial thylakoids. But I also suspect that we didn't fully
appreciate that the other photosynthetic bacteria have such different
photosynthetic membrane structures, whence the muddied specificity of the
definition and parents (it was done by me and a former TAIR curator --
neither of us experts on bacteria!).
It might be safest to use GO:0030075 as the broader 'plasma
membrane-derived photosynthetic membrane' because of the def/name
inconsistency. But if we do that, would there be any difference between
GO:0030075 and 'chromatophore' (GO:0042716, defined as "A pigment bearing
structure found in certain photosynthetic bacteria and cyanobacteria which
is derived from the cytoplasmic membrane, sometimes consisting of simple
invaginations and sometimes a complete vesicle.")? If not, they can be
merged. The other option is to dclare it to be the term for
cyanobacterial thylakoids, and rephrase the definition accordingly. Any
preference?
No matter what we do with this term, we can remove the broad synonym
'thylakoid (sensu Bacteria)' because it's a bit misleading; I'll also edit
the comment on the obsolete term 'thylakoid (sensu Bacteria)'. We can also
move 'chromatophore' from under 'vesicle', since that would fit with both
the existing definition and your comments. Can it go under 'plasma
membrane-derived photosynthetic membrane'?
Thanks again,
Midori
On Thu, 31 Jul 2008, Deborah Siegele wrote:
> Hi Midori,
>
>> From scanning the literature and talking with colleagues who work on photosynthesis, I think that the term thylakoid is used almost exclusively for the photosynthetic membranes found in chloroplasts and in cyanobacteria. Personally, I find it confusing that the word "thylakoid" is being used for all photosynthetic organisms. I think of a thylakoid as the stacked photosynthetic membranes that are characteristic of chloroplasts and cyanobacteria.
>
> I think I would modify the first sentence of the definition of GO:0009579 thylakoid to read: " A membraneous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria." Another reason for grouping these together is that chloroplasts are generally accepted to have evolved from an ancestral cyanobacterial endosymbiont.
>
> Could GO:0030075 plasma membrane-derived thylakoid be renamed? Plasma membrane-derived photosynthetic membrane is redundant, but that is all I can think of right now. What sorts of structures are supposed to be annotated to this term? that might help in naming it.
>
> I think the definition and synonyms for GO:0030075 also need to be modified. The current definition is: "A membraneous cellular structure derived from, but not necessarily continuous with, the plasma membrane. It bears the photosynthetic pigments in photosynthetic bacteria." I would change it to "A membraneous cellular structure bearing the photosynthetic apparatus that is derived from, but not necessarily continuous with, the plasma membrane of prokaryotic cells."
>
>
> [Should we add this relationship?]
> ? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
> "cytoplasmic vesicle membrane" [GO:0030659]
>
> I'm not sure that this relationship should be added,because I'm not sure that the word vesicle would be used to describe all the membraneous cellular structures bearing the photosynthetic apparatus that are found in photosynthetic prokaryotes. For example, I've attached a jpg file of a diagram of a Chlorobium tepidum cell. The picture was taken from <http://kchf-45.karlov.mff.cuni.cz/~jakub/chlorosome.htm>. I wouldn't call this structure a vesicle, but maybe my mental image of a vesicle is too restricted.
>
> Regards,
>
> Debby
>
>
>
>
>
>>>> Midori Harris <midori at ebi.ac.uk> 07/25/08 9:43 AM >>>
> Hi,
>
> Chris and I need some assistance from someone who knows about thylakoids,
> especially in prokaryotes. Chris asks (as part of SF 2019054; link below):
>
> [Should we add this relationship?]
> ? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
> "cytoplasmic vesicle membrane" [GO:0030659]
> This inference would be true if the def of PMDTM was "a M that
> sourrounds a PMDT". This would seem to be
> suggested by the text def:
> The pigmented membrane of a plasma membrane-derived thylakoid."
> However, the DAG structure suggests that the genus of the definition
> should be a *portion* of the plasma membrane that....
> The use of derivation is confusing. Do we just need to use
> derives_from in GO?
>
>> From what I've gathered from GO definitions and the wiki, some bacterial
> thylakoids are continuous with the plasma membrane (i.e. a portion of the
> plasma membrane). As a result, the GO structure and defs are kind of
> confused -- see the SF comments for more details, and let me know if you
> have any questions about our questions ...
>
> SF link:
> https://sourceforge.net/tracker/index.php?func=detail&aid=2019054&group_id=36855&atid=440764
>
> wiki page noted above:
> http://wiki.geneontology.org/index.php/Meeting_Notes_3
>
> Thanks,
> Midori
>
>
---------- Forwarded message ----------
Date: Mon, 04 Aug 2008 17:03:36 -0500
From: Deborah Siegele <siegele at mail.bio.tamu.edu>
To: midori at ebi.ac.uk
Cc: tberardi at acoma.stanford.edu, jdeegan at ebi.ac.uk, cjm at fruitfly.org,
mgiglio at som.umaryland.edu, donghui at stanford.edu, jimhu at tamu.edu
Subject: Re: thylakoid membrane question
Hi Midori,
I haven't finished digesting everything you wrote, but I do have one immediate suggestion. I think that 'plasma-membrane derived photosynthetic membrane structure' might be a better name than 'plasma-membrane derived photosynthetic membrane', which is what I first suggested.
I'll contact a colleague who works on cyanobacteria and ask whether it is accurate to give thylakoids in cyanobacteria the parent of plasma-membrane derived photosynthetic membrane.
>From what I've read, I don't think there is a difference in prokaryotes between chromatophore and photosynthetic membrane. I think the distinction comes from plants, which have plastids that synthesize and store pigments but aren't photosynthetic. In the recent literature, these plastids seems to be more commonly called chromoplasts rather than chromatophores, probably to avoid confusion with "chromatophore" used to refer to pigmented cells in animals.
Regards,
Debby
>>> Midori Harris <midori at ebi.ac.uk> 08/04/08 7:03 AM >>>
Hi Debby,
Thanks for your very informative reply, and sorry I haven't got back to it
until now. From your mail, the GO structure, and some things I've found
online, I think we should have three terms for photosynthetic membrane
structures:
- one for thylakoids in plants; 'plastid thylakoid' covers this
- one for thylakoids in cyanobacteria
- one for the photosynthetic membranes in other photosynthetic bacteria
The first two would be grouped under thylakoid (GO:0009579; I've edited
the def as you recommended). The second two can be grouped under a term
for plasma membrane-derived photosynthetic membrane -- assuming that's
biologically accurate. If not, they don't need to be grouped, and the
cyanobacterial thylakoid term can have just one parent.
In any case, all three would be descendants of the most general term,
'photosynthetic membrane' (GO:0034357).
Despite the definition wording, I think -- based on the term name and
parents -- that GO:0030075 may have been originally intended to represent
cyanobacterial thylakoids. But I also suspect that we didn't fully
appreciate that the other photosynthetic bacteria have such different
photosynthetic membrane structures, whence the muddied specificity of the
definition and parents (it was done by me and a former TAIR curator --
neither of us experts on bacteria!).
It might be safest to use GO:0030075 as the broader 'plasma
membrane-derived photosynthetic membrane' because of the def/name
inconsistency. But if we do that, would there be any difference between
GO:0030075 and 'chromatophore' (GO:0042716, defined as "A pigment bearing
structure found in certain photosynthetic bacteria and cyanobacteria which
is derived from the cytoplasmic membrane, sometimes consisting of simple
invaginations and sometimes a complete vesicle.")? If not, they can be
merged. The other option is to dclare it to be the term for
cyanobacterial thylakoids, and rephrase the definition accordingly. Any
preference?
No matter what we do with this term, we can remove the broad synonym
'thylakoid (sensu Bacteria)' because it's a bit misleading; I'll also edit
the comment on the obsolete term 'thylakoid (sensu Bacteria)'. We can also
move 'chromatophore' from under 'vesicle', since that would fit with both
the existing definition and your comments. Can it go under 'plasma
membrane-derived photosynthetic membrane'?
Thanks again,
Midori
On Thu, 31 Jul 2008, Deborah Siegele wrote:
> Hi Midori,
>
>> From scanning the literature and talking with colleagues who work on photosynthesis, I think that the term thylakoid is used almost exclusively for the photosynthetic membranes found in chloroplasts and in cyanobacteria. Personally, I find it confusing that the word "thylakoid" is being used for all photosynthetic organisms. I think of a thylakoid as the stacked photosynthetic membranes that are characteristic of chloroplasts and cyanobacteria.
>
> I think I would modify the first sentence of the definition of GO:0009579 thylakoid to read: " A membraneous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria." Another reason for grouping these together is that chloroplasts are generally accepted to have evolved from an ancestral cyanobacterial endosymbiont.
>
> Could GO:0030075 plasma membrane-derived thylakoid be renamed? Plasma membrane-derived photosynthetic membrane is redundant, but that is all I can think of right now. What sorts of structures are supposed to be annotated to this term? that might help in naming it.
>
> I think the definition and synonyms for GO:0030075 also need to be modified. The current definition is: "A membraneous cellular structure derived from, but not necessarily continuous with, the plasma membrane. It bears the photosynthetic pigments in photosynthetic bacteria." I would change it to "A membraneous cellular structure bearing the photosynthetic apparatus that is derived from, but not necessarily continuous with, the plasma membrane of prokaryotic cells."
>
>
> [Should we add this relationship?]
> ? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
> "cytoplasmic vesicle membrane" [GO:0030659]
>
> I'm not sure that this relationship should be added,because I'm not sure that the word vesicle would be used to describe all the membraneous cellular structures bearing the photosynthetic apparatus that are found in photosynthetic prokaryotes. For example, I've attached a jpg file of a diagram of a Chlorobium tepidum cell. The picture was taken from <http://kchf-45.karlov.mff.cuni.cz/~jakub/chlorosome.htm>. I wouldn't call this structure a vesicle, but maybe my mental image of a vesicle is too restricted.
>
> Regards,
>
> Debby
>
>
>
>
>
>>>> Midori Harris <midori at ebi.ac.uk> 07/25/08 9:43 AM >>>
> Hi,
>
> Chris and I need some assistance from someone who knows about thylakoids,
> especially in prokaryotes. Chris asks (as part of SF 2019054; link below):
>
> [Should we add this relationship?]
> ? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a
> "cytoplasmic vesicle membrane" [GO:0030659]
> This inference would be true if the def of PMDTM was "a M that
> sourrounds a PMDT". This would seem to be
> suggested by the text def:
> The pigmented membrane of a plasma membrane-derived thylakoid."
> However, the DAG structure suggests that the genus of the definition
> should be a *portion* of the plasma membrane that....
> The use of derivation is confusing. Do we just need to use
> derives_from in GO?
>
>> From what I've gathered from GO definitions and the wiki, some bacterial
> thylakoids are continuous with the plasma membrane (i.e. a portion of the
> plasma membrane). As a result, the GO structure and defs are kind of
> confused -- see the SF comments for more details, and let me know if you
> have any questions about our questions ...
>
> SF link:
> https://sourceforge.net/tracker/index.php?func=detail&aid=2019054&group_id=36855&atid=440764
>
> wiki page noted above:
> http://wiki.geneontology.org/index.php/Meeting_Notes_3
>
> Thanks,
> Midori
>
>
---------- Forwarded message ----------
Date: Mon, 11 Aug 2008 11:39:45 -0500
From: Deborah Siegele <siegele at mail.bio.tamu.edu>
To: midori at ebi.ac.uk
Cc: tberardi at acoma.stanford.edu, jdeegan at ebi.ac.uk, cjm at fruitfly.org,
mgiglio at som.umaryland.edu, donghui at stanford.edu, jimhu at tamu.edu
Subject: Re: thylakoid membrane question
Hi,
I spoke with Susan Golden in my department who works on photosynthesis in cyanobacteria. She says that oxygenic vs anoxygenic is the key distinction between the photosynthetic membranes of cyanobacteria/chloroplasts and other organisms and suggested that the photosynthetic membrane in prokaryotes other than cyanobacteria be called 'anoxygenic photosynthetic membrane.' Because of the evolutionary relationship and similarities between chloroplasts and cyanobacteria, she didn't like having two separate thylakoid terms for plants and cyanobacteria. She was dubious about connecting the chloroplast photosynthetic membrane to 'plasma-membrane derived photosynthetic membrane' because even though it is likely that it originates from the plasma membrane she doesn't know of any experimental evidence one way or the other.
Susan suggested some names of experts who might be interested in providing input on these GO terms: Robert Blankenship (blankenship at WUSTL.EDU), Don Bryant (dab14 at psu.edu), or Carl Bauer (bauer at indiana.edu).
By the way, I was wrong in thinking that chlorosomes were an example of photosynthetic membranes. They're light-harvesting complexes (antennas), but don't have any photosynthetic reaction centers.
Regards,
Debby
>>> Midori Harris <midori at ebi.ac.uk> 08/05/08 4:57 AM >>>
Hi Debby,
> I haven't finished digesting everything you wrote, but I do have one
> immediate suggestion. I think that 'plasma-membrane derived
> photosynthetic membrane structure' might be a better name than
> 'plasma-membrane derived photosynthetic membrane', which is what I first
> suggested.
Fine on both counts; I don't mind a bit of time to digest all this myself.
> I'll contact a colleague who works on cyanobacteria and ask whether it
> is accurate to give thylakoids in cyanobacteria the parent of
> plasma-membrane derived photosynthetic membrane.
Thanks! I'll wait for the expert reply.
Midori
>>> Midori Harris <midori at ebi.ac.uk> 08/04/08 7:03 AM >>>
Hi Debby,
Thanks for your very informative reply, and sorry I haven't got back to it
until now. From your mail, the GO structure, and some things I've found
online, I think we should have three terms for photosynthetic membrane
structures:
- one for thylakoids in plants; 'plastid thylakoid' covers this
- one for thylakoids in cyanobacteria
- one for the photosynthetic membranes in other photosynthetic bacteria
The first two would be grouped under thylakoid (GO:0009579; I've edited
the def as you recommended). The second two can be grouped under a term
for plasma membrane-derived photosynthetic membrane -- assuming that's
biologically accurate. If not, they don't need to be grouped, and the
cyanobacterial thylakoid term can have just one parent.
In any case, all three would be descendants of the most general term,
'photosynthetic membrane' (GO:0034357).
Despite the definition wording, I think -- based on the term name and
parents -- that GO:0030075 may have been originally intended to represent
cyanobacterial thylakoids. But I also suspect that we didn't fully
appreciate that the other photosynthetic bacteria have such different
photosynthetic membrane structures, whence the muddied specificity of the
definition and parents (it was done by me and a former TAIR curator --
neither of us experts on bacteria!).
It might be safest to use GO:0030075 as the broader 'plasma
membrane-derived photosynthetic membrane' because of the def/name
inconsistency. But if we do that, would there be any difference between
GO:0030075 and 'chromatophore' (GO:0042716, defined as "A pigment bearing
structure found in certain photosynthetic bacteria and cyanobacteria which
is derived from the cytoplasmic membrane, sometimes consisting of simple
invaginations and sometimes a complete vesicle.")? If not, they can be
merged. The other option is to dclare it to be the term for
cyanobacterial thylakoids, and rephrase the definition accordingly. Any
preference?
No matter what we do with this term, we can remove the broad synonym
'thylakoid (sensu Bacteria)' because it's a bit misleading; I'll also edit
the comment on the obsolete term 'thylakoid (sensu Bacteria)'. We can also
move 'chromatophore' from under 'vesicle', since that would fit with both
the existing definition and your comments. Can it go under 'plasma
membrane-derived photosynthetic membrane'?
Thanks again,
Midori
---------- Forwarded message ----------
Date: Tue, 5 Aug 2008 10:57:19 +0100 (BST)
From: Midori Harris <midori at ebi.ac.uk>
To: Deborah Siegele <siegele at mail.bio.tamu.edu>
Cc: tberardi at acoma.stanford.edu, jdeegan at ebi.ac.uk, cjm at fruitfly.org,
mgiglio at som.umaryland.edu, donghui at stanford.edu, jimhu at tamu.edu
Subject: Re: thylakoid membrane question
Hi Debby,
> I haven't finished digesting everything you wrote, but I do have one
> immediate suggestion. I think that 'plasma-membrane derived photosynthetic
> membrane structure' might be a better name than 'plasma-membrane derived
> photosynthetic membrane', which is what I first suggested.
Fine on both counts; I don't mind a bit of time to digest all this myself.
> I'll contact a colleague who works on cyanobacteria and ask whether it is
> accurate to give thylakoids in cyanobacteria the parent of plasma-membrane
> derived photosynthetic membrane.
Thanks! I'll wait for the expert reply.
Midori
---------- Forwarded message ----------
Date: Wed, 13 Aug 2008 13:54:10 +0100 (BST)
From: Midori Harris <midori at ebi.ac.uk>
To: Deborah Siegele <siegele at mail.bio.tamu.edu>
Cc: tberardi at acoma.stanford.edu, jdeegan at ebi.ac.uk, cjm at fruitfly.org,
mgiglio at som.umaryland.edu, donghui at stanford.edu, jimhu at tamu.edu
Subject: Re: thylakoid membrane question
Hi Debby,
On Mon, 11 Aug 2008, Deborah Siegele wrote:
> Hi,
>
> I spoke with Susan Golden in my department who works on photosynthesis in
> cyanobacteria. She says that oxygenic vs anoxygenic is the key distinction
> between the photosynthetic membranes of cyanobacteria/chloroplasts and other
> organisms and suggested that the photosynthetic membrane in prokaryotes other
> than cyanobacteria be called 'anoxygenic photosynthetic membrane.' Because of
> the evolutionary relationship and similarities between chloroplasts and
> cyanobacteria, she didn't like having two separate thylakoid terms for plants
> and cyanobacteria.
I understand, but I think for GO purposes we can't really avoid having two
terms, because of the differences in location: plant thylakoids are located in
plastids, whereas cyanobacteria have no plastids. So we have two separate
terms, both of which are subtypes of the general 'thylakoid' term, one for
thylakoids in plastids and one for thylakoids not found as parts of plastids.
> She was dubious about connecting the chloroplast photosynthetic membrane to
> 'plasma-membrane derived photosynthetic membrane' because even though it is
> likely that it originates from the plasma membrane she doesn't know of any
> experimental evidence one way or the other.
OK; in that case it would be safer for GO not to make any connection between
'plastid thylakoid' and 'plasma-membrane derived photosynthetic membrane'.
That's no problem.
> Susan suggested some names of experts who might be interested in providing
> input on these GO terms: Robert Blankenship (blankenship at WUSTL.EDU), Don
> Bryant (dab14 at psu.edu), or Carl Bauer (bauer at indiana.edu).
Excellent! I'll get in touch if any further questions come up. I think my
initial questions are more or less in hand now.
> By the way, I was wrong in thinking that chlorosomes were an example of
> photosynthetic membranes. They're light-harvesting complexes (antennas), but
> don't have any photosynthetic reaction centers.
OK, I'll make sure that is reflected in the ontology (all I'll have to "do" is
leave it as is).
Thanks again for all your help,
Midori
>
> Regards,
>
> Debby
>
>
>
>>>> Midori Harris <midori at ebi.ac.uk> 08/05/08 4:57 AM >>>
> Hi Debby,
>
>> I haven't finished digesting everything you wrote, but I do have one
>> immediate suggestion. I think that 'plasma-membrane derived
>> photosynthetic membrane structure' might be a better name than
>> 'plasma-membrane derived photosynthetic membrane', which is what I first
>> suggested.
>
> Fine on both counts; I don't mind a bit of time to digest all this myself.
>
>> I'll contact a colleague who works on cyanobacteria and ask whether it
>> is accurate to give thylakoids in cyanobacteria the parent of
>> plasma-membrane derived photosynthetic membrane.
>
> Thanks! I'll wait for the expert reply.
>
> Midori
>
>>>> Midori Harris <midori at ebi.ac.uk> 08/04/08 7:03 AM >>>
> Hi Debby,
>
> Thanks for your very informative reply, and sorry I haven't got back to it
> until now. From your mail, the GO structure, and some things I've found
> online, I think we should have three terms for photosynthetic membrane
> structures:
>
> - one for thylakoids in plants; 'plastid thylakoid' covers this
> - one for thylakoids in cyanobacteria
> - one for the photosynthetic membranes in other photosynthetic bacteria
>
> The first two would be grouped under thylakoid (GO:0009579; I've edited
> the def as you recommended). The second two can be grouped under a term
> for plasma membrane-derived photosynthetic membrane -- assuming that's
> biologically accurate. If not, they don't need to be grouped, and the
> cyanobacterial thylakoid term can have just one parent.
>
> In any case, all three would be descendants of the most general term,
> 'photosynthetic membrane' (GO:0034357).
>
> Despite the definition wording, I think -- based on the term name and
> parents -- that GO:0030075 may have been originally intended to represent
> cyanobacterial thylakoids. But I also suspect that we didn't fully
> appreciate that the other photosynthetic bacteria have such different
> photosynthetic membrane structures, whence the muddied specificity of the
> definition and parents (it was done by me and a former TAIR curator --
> neither of us experts on bacteria!).
>
> It might be safest to use GO:0030075 as the broader 'plasma
> membrane-derived photosynthetic membrane' because of the def/name
> inconsistency. But if we do that, would there be any difference between
> GO:0030075 and 'chromatophore' (GO:0042716, defined as "A pigment bearing
> structure found in certain photosynthetic bacteria and cyanobacteria which
> is derived from the cytoplasmic membrane, sometimes consisting of simple
> invaginations and sometimes a complete vesicle.")? If not, they can be
> merged. The other option is to dclare it to be the term for
> cyanobacterial thylakoids, and rephrase the definition accordingly. Any
> preference?
>
> No matter what we do with this term, we can remove the broad synonym
> 'thylakoid (sensu Bacteria)' because it's a bit misleading; I'll also edit
> the comment on the obsolete term 'thylakoid (sensu Bacteria)'. We can also
> move 'chromatophore' from under 'vesicle', since that would fit with both
> the existing definition and your comments. Can it go under 'plasma
> membrane-derived photosynthetic membrane'?
>
> Thanks again,
> Midori
>
>
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