[Ontology-editors] bacterial cell envelopes (fwd)

Wed Jul 29 06:52:02 PDT 2009

forwarding for archiving

---------- Forwarded message ----------
Date: Tue, 28 Jul 2009 17:27:13 -0400
From: "Gwinn Giglio, Michelle" <mgiglio at som.umaryland.edu>
To: Midori Harris <midori at ebi.ac.uk>
Cc: Deborah Siegele <siegele at mail.bio.tamu.edu>
Subject: Re: bacterial cell envelopes

That sounds fine to me.

:)

Michelle

On 7/28/09 7:41 AM, "Midori Harris" <midori at ebi.ac.uk> wrote:

> Hi Debby & Michelle,
>
> Thanks for your comments. It sounds as though we should change the
> definition and relationships in GO so that the cell envelope includes the
> plama membrane, although this interpretation is not quite universal.
>
> Since we're deciding that the cell envelope always includes the plasma
> membrane, and we're about to introduce the has_part relationship in the
> component ontology, we can avoid adding yucky terms like "cell envelope
> plasma membrane". Instead, we can just add the relationship cell envelope
> has_part plasma membrane. The relationship would be stripped (along with
> all has_part links) from several of the released GO files, but would be
> kept in the editors' file and the "extended" GO file
> (gene_ontology_ext.obo).
>
> How does that sound? If it's OK, I can implement it rate this week or
> early next week.
>
> Midori
>
> On Thu, 23 Jul 2009, Gwinn Giglio, Michelle wrote:
>
>>
>>
>> Hi all,
>>
>> I've been monitoring the SF item and had planned to chime in at some point,
>> but I guess I hoped Midori's first response would resolve things - no such
>> luck.  :)
>>
>> When these terms were first made I consulted textbooks and it was there that
>> I saw the plasma membrane excluded from the cell envelope which is why we
>> defined it that way.  I did a quick search just now and found it excluded in
>> the description in Medical Microbiology which would support the current
>> definition. Found it excluded in some web sources and included in others. I
>> no longer have the textbooks I used originally.
>>
>> When I first looked this up many years ago - it seemed that people didn't
>> use the phrase "cell envelope" when referring to Gram + bugs.
>>
>> Perhaps things have changed in the many (getting close to 10) years since I
>> originally looked at this stuff.
>>
>> I don't feel strongly one way or the other - but since all cells do not have
>> envelopes we would have to create plasma membrane child terms to go under
>> cell envelope - "cell envelope plasma membrane" or something like that.
>> Which I don't like.  It causes confusion. But if we have to we have to.
>>
>> I'm just not sure there is clear agreement on the definition of this term in
>> the community.  But I agree that it seems like the membrane should be part
>> of the envelope.
>>
>> Michelle
>>
>>
>>
>>
>>
>> On 7/23/09 11:57 AM, "Deborah Siegele" <siegele at mail.bio.tamu.edu> wrote:
>>
>>> Hi Midori and Michelle,
>>>
>>> I think the most common usage for the cell envelope of prokaryotic cells
>>> includes the cytoplasmic membrane.  I checked two widely used Microbiology
>>> textbooks and they both include the cytoplasmic membrane in the cell
>>> envelope
>>> of all bacteria and archaea.  In papers on E. coli (a representative
>>> Gram-neg.
>>> bacterium), envelope includes the cytoplasmic membrane. In a google scholar
>>> search, the papers I found on gram-pos. bacteria focused on the 'cell wall
>>> envelope'.  I can email colleagues who work on Gram-pos. bacteria and get
>>> feedback from them.
>>>
>>> Cheers,
>>>
>>> Debby
>>>
>>>
>>>>>> Midori Harris <midori at ebi.ac.uk> 07/23/09 5:11 AM >>>
>>> Hi Michelle & Debby,
>>>
>>> The question of whether the GO CC term "cell envelope" (GO:0030313) should
>>> include or exclude the cytoplasmic membrane came up back in late 2005, and
>>> has now arisen again in SF 2824719. (I'm replying to email from the
>>> earlier occasion to refresh Michelle's memory and give Debby some
>>> background.)
>>>
>>> https://sourceforge.net/tracker/?func=detail&aid=2824719&group_id=36855&atid
>>> =4
>>> 40764
>>>
>>> At present, the "cell envelope" definition (as hashed out even longer ago,
>>> mostly by Michelle with a tiny bit of help from me) excludes the
>>> cytoplasmic membrane, and therefore fits the definition of its parent
>>> "external encapsulating structure".
>>>
>>> Now that the question has come up again, we can either leave things as
>>> they are, or modify the "cell envelope" definition to include the
>>> cytoplasmic membrane; if we change the definition, we'll also want to
>>> change the parentage because "external encapsulating structure" excludes
>>> the cytoplasmic/plasma membrane.
>>>
>>> Which do you think would better suit you and the prok community(-ies)?
>>>
>>> Thanks,
>>> Midori
>>>
>>> On Wed, 21 Dec 2005, Midori Harris wrote:
>>>
>>>> Hi Michelle,
>>>>
>>>> I've decided to leave the cell envelope terms as theey are for now. If a
>>>> need for a Gram-positive cell envelope term arises, we can add it, but I
>>>> won't bother to do it 'on spec', since the current arrangement works for
>>>> you.
>>>>
>>>> Midori
>>>>
>>>> On Thu, 1 Dec 2005, Midori Harris wrote:
>>>>
>>>>> Hi Michelle,
>>>>>
>>>>> Thanks for the prompt response! I'll plunk your comments into the SF item,
>>>>> and see if there's any reply. If you think the existing terms are
>>>>> sufficient, we don't have to add anything -- in particular, if Gram
>>>>> positives don't have cell envelopes, then cell envelope is the same as
>>>>> cell envelope (sensu Gram negative), and one term will do. And if you want
>>>>> to leave the plasma membrane out of the cell envelope definition, that's
>>>>> fine with me.
>>>>>
>>>>> The curator who suggested the terms is at TAIR, and therefore presumably
>>>>> mainly a plant person. That doesn't mean she can't also know about
>>>>> bacteria, of course, but it does mean I won't assume she knows more than
>>>>> you!
>>>>>
>>>>> Midori
>>>>>
>>>>> On Thu, 1 Dec 2005, Michelle Gwinn Giglio wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> Hi Midori,
>>>>>>
>>>>>> I can live with expanding the definition of cell envelope to include the
>>>>>> cytoplasmic membrane, but otherwise I like the GO definition better and
>>>>>> in fact it should actually be expanded.  The proposed definition below
>>>>>> leaves out a key part of the envelope which is the periplasmic space.
>>>>>> An important part of the current GO def is that it says "everything"
>>>>>> outside the cell membrane, rather than restricting the def to just a few
>>>>>> named things.  There are layers of LPS, protein, and phospholipids that
>>>>>> are part of the Gram negative envelope.  In fact the term "cell
>>>>>> envelope" in my experience is only used with Gram negatives, and that is
>>>>>> what my textbook says.  But I have seen instances of its use with
>>>>>> positives, even though I don't think its technically correct.  So, I'm
>>>>>> not sure there should really be a Gram positive envelope term, but I'm
>>>>>> not sure enough to oppose it.
>>>>>>
>>>>>> How about this:
>>>>>>
>>>>>> cell envelope
>>>>>> Everything external to and including the cytoplasmic membrane of
>>>>>> bacteria, including, but not limited to, the periplasmic space, cell
>>>>>> wall, and outer membrane if present.
>>>>>>
>>>>>> cell envelope Gram negative
>>>>>> Everything external to and including the cytoplasmic membrane of Gram
>>>>>> negative bacteria, including, but not limited to, the periplasmic space,
>>>>>> cell wall, and outer membrane.
>>>>>>
>>>>>> cell envelope Gram positive
>>>>>> Everything external to and including the cytoplasmic membrane of Gram
>>>>>> positive bacteria, including the cell wall.
>>>>>>
>>>>>> Michelle
>>>>>>
>>>>>>
>>>>>>
>>>>>> Midori Harris wrote:
>>>>>>
>>>>>>> Hi Michelle,
>>>>>>>
>>>>>>> We've had some suggestions from a TAIR curator for some changes and
>>>>>>> additions in the 'cell envelope' terms for bacteria. I said that we
>>>>>>> would
>>>>>>> need your input before we make any changes, ince we got the existing
>>>>>>> terms
>>>>>>> and definitions from you. So could you please comment on these
>>>>>>> suggestions? The fist seems to be a different definition from the
>>>>>>> existing
>>>>>>> cell evelope, and the other two are proposed new terms.
>>>>>>>
>>>>>>> term: cell envelope (sensu Bacteria)
>>>>>>> definition: The cell envelope of a bacteria is defined as the cell
>>>>>>> membrane (plasma membrane) and cell wall plus an outer membrane if one
>>>>>>> is
>>>>>>> present.
>>>>>>> definition_reference:  HYPERLINK
>>>>>>> "http://www.med.sc.edu:85/fox/cell_envelope.htm"
>>>>>>> http://www.med.sc.edu:85/fox/cell_envelope.htm
>>>>>>> comment: GO definition of cell envelope does not include the cell
>>>>>>> membrane.
>>>>>>>
>>>>>>> term: cell envelope (sensu Gram-negative Bacteria)
>>>>>>> definition: The cell envelope of an Gram-negative bacteria includes the
>>>>>>> cell membrane (plasma membrane) and cell wall plus the outer membrane.
>>>>>>>
>>>>>>> term: cell envelope (sensu Gram-positive Bacteria)
>>>>>>> definition: The cell envelope of an Gram-positive bacteria includes the
>>>>>>> cell membrane (plasma membrane) and cell wall.
>>>>>>>
>>>>>>> The request is a small part of SF 1284217.
>>>>>>> https://sourceforge.net/tracker/index.php?func=detail&aid=1284217&group_
>>>>>>> id
>>>>>>> =36855&atid=440764
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Midori
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>