plasmid SO:0000155 [sf#73]

[srynobio]

Reported by srengel on 2008-01-10 21:10 UTC hi, would it be possible for 'plasmid' to be pulled out from under 'reagent', so that it is simply under 'region' at the same level as, and as a sibling to, 'chromosome'?

we're asking because some organisms have naturally occurring plasmids, that are annotatable, but not as 'reagents'.

for example, at SGD, we have the 2-micron plasmid, which is a naturally-occurring circle of DNA distinct from chromosomes. we have annotated the 2-micron plasmid, and have included it in our GFF3. it is currently in our GFF as 'region'. it seems most appropriate to use the SO term 'plasmid', but not necessarily with 'plasmid' being a child of 'reagent'.

thanks, stacia

[srynobio]

Commented by mlgwinn on 2008-01-11 14:39 UTC Logged In: YES user_id=482944 Originator: NO

Hi,

I agree plasmid should be at the same level as chromosome. There are hundreds and hundreds of known (and many more yet to be discovered) naturally occurring plasmids in bacterial genomes, some linear, some circular. Some natural plasmids have been engineered into reagents but that is certainly not their role in the wild. They are very important players in prokaryotic biology.

Michelle

[srynobio]

Commented by batchelorc on 2008-01-12 12:17 UTC Logged In: YES user_id=1473024 Originator: NO

Hello,

plasmid is also a extrachromosomal_mobile_genetic_element (SO:0001038)---is this OK?

The workshop on plasmids, phages, transposons and other mobile elements in 2006 dealt with lots of this sort of thing (http://www.sequenceontology.org/workshop.shtml), but the notes do acknowledge plasmid being a reagent as an unresolved problem.

Perhaps we could make "reagent" an attribute rather than a parent. Then we could make a new term plasmid_reagent, which would be defined as a plasmid used as a reagent.

Best wishes, Colin.

[srynobio]

Commented by eilbeck on 2008-01-14 18:24 UTC Logged In: YES user_id=742851 Originator: NO

Hi all, Plasmid is also a kind of mobile genetic element. If you use the dagview plugin you can see this more clearly. I think Colin's suggestion of making reagent a quality/attribute solves this problem.

--Karen

[srynobio]

Commented by srengel on 2008-01-14 18:32 UTC Logged In: YES user_id=785556 Originator: YES

hi, i haven't commented on the bit about making 'reagent' an 'attribute' and whether or not that would work because i'm not quite sure how attributes are used (ex., for a different issue, separate from this plasmid stuff entirely, we would like to use the term 'plus 1 translational frameshift' as a locatable sequence feature, but we see that it's an 'attribute' instead of a 'feature', which has left us nonplussed).

re. the extrachromosomal MGE 1038, i think that's ok. the def of its parent 1037 made me pause, but i was able to convince myself that it's ok. i sure would like to hear what Michelle thinks.

stacia

[srynobio]

Commented by mlgwinn on 2008-01-14 19:02 UTC Logged In: YES user_id=482944 Originator: NO

Hi,

There are two things that concern me. First not all plasmids are mobile. Many, perhaps most, plasmids can not make themselves move from cell to cell. So, perhaps you would want a new term "conjugal_plasmid" that is a child of "plasmid" and "extrachromosomal_mobile_genetic_element" and regular "plasmid" would be a child of just "extrachromosomal_genetic_element" (which doesn't seem to exist).

And, although I don't understand how the attributes work either, it seems wrong to me to have "reagent" an attribute of the term "plasmid". I see that there is a child of plasmid that is "engineered_plasmid". I think this one can have the "reagent" attribute and/or be a child of "reagent". But regular plasmid should not be linked to the concept of reagent. This is a misconception of the role that plasmids play in the living world.

Michelle

[srynobio]

Commented by eilbeck on 2008-01-14 19:10 UTC Logged In: YES user_id=742851 Originator: NO

Does plasmid is_a replicon work for any of you guys?

[srynobio]

Commented by srengel on 2008-01-14 19:19 UTC Logged In: YES user_id=785556 Originator: YES

hi, replicon isn't a term i use or am familiar with. i've done some quick searches to see how it is used, so i think i understand what it's supposed to convey.

so then my questions are these: what value would it add?
what would be its placement in the ontology?
what would be its definition?
are we sure that all plasmids replicate from a single ORI?
are there any plasmids that have dual (or more) origins?

stacia

[srynobio]

Commented by mlgwinn on 2008-01-14 19:33 UTC Logged In: YES user_id=482944 Originator: NO

Hi,

Yes, a plasmid is a replicon, absolutely.

In my understanding of the use of replicon, it doesn't matter if there is one or more origins, just that the piece of DNA can replicate itself so has at least one origin.

However, having plasmid is_a replicon doesn't change any of the other issues concerning reagent and mobile genetic element. Right?

Michelle

[srynobio]

Commented by eilbeck on 2008-01-14 20:23 UTC Logged In: YES user_id=742851 Originator: NO

We need to establish the correct is_a parent for the term plasmid. When that is done - we can then sort out the remaining issues. --K

[srynobio]

Commented by srengel on 2008-01-14 20:26 UTC Logged In: YES user_id=785556 Originator: YES

what is wrong with it just being at the same level as chromosome? so it would be this:

is_a: SO:0000001 ! region

stacia

[srynobio]

Commented by mlgwinn on 2008-01-14 20:40 UTC Logged In: YES user_id=482944 Originator: NO

Hi,

Ah, yes, I see. Well, in addition to being is_a replicon, it is also is_a extrachromosomal genetic element (although I couldn't find that term).

Michelle

[srynobio]

Commented by mlgwinn on 2008-01-14 21:31 UTC Logged In: YES user_id=482944 Originator: NO

Hi, I didn't see Stacia's comment before adding mine - email glitch I think. But I agree it seems like it could work that way too.

Michelle

[srynobio]

Commented by batchelorc on 2008-01-15 12:14 UTC Logged In: YES user_id=1473024 Originator: NO

mlgwinn writes:

> First not all plasmids are mobile. > Many, perhaps most, plasmids can not make themselves move from cell to cell.

But do they all have intra-genome mobility, which is the other half of the mobile_genetic_element (SO:0001037) definition?

Would it make sense for chromosome (SO:0000340) to be a child of replicon, as per the Summers diagram from the MGE workshop? (In tracker item 1855721 I suggested "A region containing a unique origin of replication and a unique termination site." but probably "A region containing at least one origin of replication and a corresponding termination site." would be better.)

Best wishes, Colin.

[srynobio]

Commented by batchelorc on 2008-01-15 12:26 UTC Logged In: YES user_id=1473024 Originator: NO

Stacia Engel writes:

> we would like to use the term 'plus 1 translational frameshift' > as a locatable sequence feature, but we see that it's an 'attribute' > instead of a 'feature', which has left us nonplussed

Hello,

I've created this as a new tracker item (1871918) so it can be kept track of.

Best wishes, Colin.

[srynobio]

Commented by mlgwinn on 2008-01-15 16:31 UTC Logged In: YES user_id=482944 Originator: NO

Hi,

I'm not sure what "intra-genome mobility" means - I'm guessing it means that the plasmid (or other molecule) can integrate into the chromosome?

Not all plasmids can integrate. Most remain stable independent entities.

Michelle

[srynobio]

Commented by srengel on 2008-01-16 18:41 UTC Logged In: YES user_id=785556 Originator: YES

i'm not sure that chromosome needs to be a child of replicon. even with the updated def to say 'A region containing at least one origin of replication and a corresponding termination site.'

not all origins fire at every cell cycle, therefore, termination sites will vary. it could work if the part about termination sites was removed altogether. is something about termination sites absolutely necessary?

also, i think the mobile_genetic_element aspect needs to be dropped entirely with respect to plasmid.

i do like Michelle's term 'extrachromosomal genetic element'. perhaps we should add that.

i guess we could have something like this: -replicon --chromosome --extrachromosomal_genetic_element ---plasmid

[srynobio]

Commented by mlgwinn on 2008-01-16 19:00 UTC Logged In: YES user_id=482944 Originator: NO

HI,

I don't think all extrachromosomal genetic elements are replicons though - as I think transposons would fall in this category too - don't they?

How about this:

replicon --chromosome --plasmid

extrachromosomal genetic element --plasmid --mobile extrachromosomal genetic element ----transposon

Michelle

[srynobio]

Commented by srengel on 2008-01-17 17:58 UTC Logged In: YES user_id=785556 Originator: YES

are transposons ever not part of a chromosome? that is, are they ever just floating around in a nucleus on their own? i'm just not clear on that point. if yes, then having them be is-a mobile extrachromosomal genetic element is ok, if not, then not. i just don't know.

stacia