#10156 definition of primosome

[Birgit Meldal]

Hi,

I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.

Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)

Thanks,
Birgit

[Birgit Meldal]

For eukaryotes there are also components to go with these processes:

GO:0005656 pre-replicative complex, which is child_of
GO:0031261 DNA replication preinitiation complex

which explains why there are 2 processes associated with this! However, I still think it would be nice to have parental terms that apply to the whole taxonomic range.

[Jim Hu]

The primosome is part of the preinitiation complex, but travels with the DNA polymerase holoenzyme during the elongation phase of replication. The primosome is a multi-protein complex needed to lay down primers for Okazaki fragments.

http://en.wikipedia.org/wiki/Primosome

[Birgit Meldal]

Hi Jim,
The primosome is formed before the DNA polymerase joins up with the oriC and its function is more wide-reaching than just making primers for the Okasaki fragments. It acts during both, replication initiation and restart of replication after a stalled replication fork. I have spent weeks trying to get to the bottom of the definition and the wikipedia entry gets the replication initiation and restart of replication processes mixed up.
The core of the primosome is the helicase and primase but it also contains a bunch of accessory proteins. My question is, can we extend the definition of pre-replicative complex to include prokaryote complexes? If yes, I don't have to define a new parent term for all the complexes that are part of the replication initiation which I am currently curating (for the new Complex Portal in IntAct).

References (pmids):
21856207 (review)
16677308
17588514
17139333
8663105
18179598 (introduction)

Regards,
Birgit

[Jane Lomax]

Hi Becky - could you deal with this first tomorrow please? There's a pending term for 'primosome complex' in FF, I've asked Paola not to commit it until this ticket is sorted. Ta.

[Jim Hu]

I would say yes, this can be extended to prokaryotes.

[RFoulger]

Morning,

To summarise the existing Eukaryotic GO terms (see PMID:23075259, also):

pre-RI
DNA replication preinitiation complex ; GO:0031261
DNA replication preinitiation complex assembly ; GO:0071163

pre-RC
pre-replicative complex ; GO:0005656
pre-replicative complex assembly ; GO:0006267

The pre-RI complex is formed by the assembly of additional proteins onto an existing pre-RC complex:
DNA replication preinitiation complex ; GO:0031261 HAS_PART pre-replicative complex ; GO:0005656

Both CC terms have Eukaryotic taxon constraints due to their nuclear_part parentage. If we were to widen the definitions to include Prokaryotes, we'd loose this nuclear information. So we'd probably end up creating separate Euk and Prok terms anyway, whatever we call them. Therefore I'm inclined to create a separate replisome term for Prokaryotes (as currently logged in TermGenie).

Should the TG replisome term be is_a: protein-DNA complex ; GO:0032993 (similar to the existing pre-RC term, rather than just is_a: protein complex)?

thanks,
Becky

[Jim Hu]

It seems to me that the current definitions of many of these terms are way too specific, not only in nuclear parentage but also in naming components and specification of timing (e.g. in GO:0005656 ! pre-replicative complex).

IMO, the basic terms should be agnostic as to taxonomy and organellar location, and the specification of nuclear etc. should be by intersection below the agnostic terms. This may be functionally equivalent to "creating separate Euk and Prok terms anyway" but how this is done matters. In other words, agnostic terms should be create between protein complex and the current terms discussed above, and all current terms with "eukarotic chromosome" in their definitions should be children of their taxon/location-agnostic equivalents.

My concern is more general, so I will try to compose something for discussion on GO-discuss.

[Birgit Meldal]

Hi Jim and Becky,

Thank you for your responses. I will leave the issue in your hands for
now. I agree that a more hierarchial parentage would be very helpful!

Just one note, the GO:0030894 replisome term is ok as it is agnostic, it's
the primosome term that I was trying to define in TG free form.

Becky, I'm at our Hackathon at The Nucleus for the rest of the week and on
a course on Tuesday so you might not find me next door (except for first
thing in the morning) but I will try to keep an eye on my emails.

Regards,
Birgit

It seems to me that the current definitions of many of these terms are way
too specific, not only in nuclear parentage but also in naming components
and specification of timing (e.g. in GO:0005656 ! pre-replicative
complex).

IMO, the basic terms should be agnostic as to taxonomy and organellar
location, and the specification of nuclear etc. should be by intersection
below the agnostic terms. This may be functionally equivalent to "creating
separate Euk and Prok terms anyway" but how this is done matters. In other
words, agnostic terms should be create between protein complex and the
current terms discussed above, and all current terms with "eukarotic
chromosome" in their definitions should be children of their
taxon/location-agnostic equivalents.

My concern is more general, so I will try to compose something for
discussion on GO-discuss.

---

[ontology-requests:#10156] definition of primosome

Status: open
Labels: Other term-related request
Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal
Last Updated: Wed May 01, 2013 08:48 AM UTC
Owner: RFoulger

Hi,

I requested a term for the primosome on Friday but now saw that there are
already names in the ontology biological process lineage that refer to
this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they are
entirely parallel in the ontology and don't really differ in their
definition.

Although they refer to eukaryotic replication it looks as if they could
also be applicable to prokaryote replication. In that case we could call
the primosome complex either pre-replicative complex or replication
preinitiation complex. I would probably prefer pre-replicative complex as
then it can also refer to the complexes formed during restart of
replication at a stalled replication fork (see SF request 3612171)

Thanks,
Birgit

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[RFoulger]

Okay, so the simplest action is to make a taxon-agnostic grouping term for a Prokaryotic primosome term, and the Eukaryotic pre-RC and pre-RI terms:

protein-DNA complex ; GO:0032993
--[isa]replication origin complex ; GO:NEW
----[isa]primosome ; GO:NEW (submitted to TG))
----[isa]pre-replicative complex ; GO:0005656 (pre-RC)
------[HAS_PART]DNA replication preinitiation complex ; GO:0031261 (pre-RI)

replication origin complex ; GO:NEW
A protein-DNA complex that forms at the origin of replication or at the sites of replication restart, and is required for replication initiation or replication re-initiation.

Any naming/wording suggestions gratefully received.

Becky

[Birgit Meldal]

Hi Becky,

It's a good start but I think the higher order hierarchies need more
revision. For starters the GO:0031261 DNA replication preinitiation
complex is described as a protein-DNA complex but is child of protein
complex. I also feel that you switched the pre-RC and pre-RI around, at
least in comparison to the hierarchy view. On top of that the GO:0030894
replisome doesn't seem to be in the same hierarchy... I'm in a meeting
again for most of the day and at a workshop on Tuesday. I will try and
catch you whether this afternoon or on Wednesday. I think it will be
easier to sit down together and sort out all the relationships :)

Thanks,
Birgit

On 02/05/2013 12:28, RFoulger wrote:

Okay, so the simplest action is to make a taxon-agnostic grouping term
for a Prokaryotic primosome term, and the Eukaryotic pre-RC and pre-RI
terms:

protein-DNA complex ; GO:0032993
--[isa]replication origin complex ; GO:NEW
----[isa]primosome ; GO:NEW (submitted to TG))
----[isa]pre-replicative complex ; GO:0005656 (pre-RC)
------[HAS_PART]DNA replication preinitiation complex ; GO:0031261
(pre-RI)

replication origin complex ; GO:NEW
A protein-DNA complex that forms at the origin of replication or at
the sites of replication restart, and is required for replication
initiation or replication re-initiation.

Any naming/wording suggestions gratefully received.

Becky

---

[ontology-requests:#10156]
http://sourceforge.net/p/geneontology/ontology-requests/10156/
definition of primosome

Status: open
Labels: Other term-related request
Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal
Last Updated: Wed May 01, 2013 01:45 PM UTC
Owner: RFoulger

Hi,

I requested a term for the primosome on Friday but now saw that there
are already names in the ontology biological process lineage that
refer to this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they are
entirely parallel in the ontology and don't really differ in their
definition.

Although they refer to eukaryotic replication it looks as if they
could also be applicable to prokaryote replication. In that case we
could call the primosome complex either pre-replicative complex or
replication preinitiation complex. I would probably prefer
pre-replicative complex as then it can also refer to the complexes
formed during restart of replication at a stalled replication fork
(see SF request 3612171)

Thanks,
Birgit

---

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--

Dr. Birgit Meldal
IntAct Curator
European Bioinformatics Insitute
Welcome Trust Sanger Centre
Hinxton
Cambridgeshire
CB10 1SD

+44 1223 494107
bmeldal@ebi.ac.uk
http://www.ebi.ac.uk/intact/

[RFoulger]

There are pre-RCs in Proks, Euks and Archaea. So (in line with how we've done it for the ORC in GO), I will rename the existing GO:0005656 pre-RC term and create Prokaryotic and taxon-generic terms:

protein-DNA complex ; GO:0032993
--[isa]pre-replication complex (pre-RC) ; GO:NEW1 (Taxon AGNOSTIC)
----[isa]nuclear pre-replication complex ; GO:0005656 (RENAMED, EUKARYOTIC)
----[isa]DnaA pre-replication complex ; GO:NEW (PROKARYOTIC)

pre-replication complex ; GO:NEW1 (Taxon AGNOSTIC)
A protein complex that forms at the origin of replication during the initial step of DNA replication and allows the origin to become competent, or 'licensed', for replication.
is_a: protein-DNA complex
Wikipedia: Pre-replication_complex

DnaA pre-replication complex ; GO:NEW2 (PROKARYOTIC)
A protein-DNA complex containing the initiator protein DnaA bound to high-affinity recognition sites in the origin of replication, oriC.
synonym: prokaryotic pre-RC (Wikipedia: Pre-replication_complex)
PMID:19833870

All the pre-RI literature I've found is Eukaryotic, so I shall leave that term alone.

Which brings us full-circle back to the question of how the primosome fits in with the pre-RC terms. From the literature, the primosome appears to be further downstream from the pre-RC. I will move 'primosome complex ; GO:1990077' to be is_a: protein-DNA complex, and for now leave it as a sibling term to the new generic pre-RC term.

I will update the process 'complex assembly' terms to match.

Will do edits on Thursday morning if there's no objections. I'm off tomorrow (Tues) but will be back in Wednesday.
Thanks,
Becky

[RFoulger]

All the pre-RI literature I've found is Eukaryotic, so I shall leave that term alone.
should read:
All the pre-IC literature I've found is Eukaryotic, so I shall leave that term alone.

Other parentage edits I've done:
primosome complex ; GO:1990077
- is_a: protein complex ; GO:0043234
+ is_a: protein-DNA complex ; GO:0032993

DNA replication preinitiation complex ; GO:0031261 (pre-IC)
- is_a: protein complex ; GO:0043234
+ is_a: protein-DNA complex ; GO:0032993

[Jim Hu]

My understanding is that the analogous complexes in bacteria and viruses use different names but are functionally equivalent. I will email one of my friends who is a replication expert to ask about this.

Jim

On May 13, 2013, at 11:30 AM, RFoulger wrote:

All the pre-RI literature I've found is Eukaryotic, so I shall leave that term alone.
should read:
All the pre-IC literature I've found is Eukaryotic, so I shall leave that term alone.

Other parentage edits I've done:
primosome complex ; GO:1990077
- is_a: protein complex ; GO:0043234
+ is_a: protein-DNA complex ; GO:0032993

DNA replication preinitiation complex ; GO:0031261 (pre-IC)
- is_a: protein complex ; GO:0043234
+ is_a: protein-DNA complex ; GO:0032993

[ontology-requests:#10156] definition of primosome

Status: open
Labels: Other term-related request
Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal
Last Updated: Mon May 13, 2013 03:46 PM UTC
Owner: RFoulger

Hi,

I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.

Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)

Thanks,
Birgit

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=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054

[Birgit Meldal]

Thanks, Jim. That would be great! I am only curating the E. coli
complexes at the moment (got to start somewhere...). Becky and I came to
the conclusion that most people would intuitively regard the replication
preinitiation complex and the primosome as functionally homologous
complexes. Similarly, the pre-replicative complex would be the
equivalent to the DnaA-oriC complex. Different structures, same function.

Birgit

On 13/05/2013 19:09, Jim Hu wrote:

My understanding is that the analogous complexes in bacteria and
viruses use different names but are functionally equivalent. I will
email one of my friends who is a replication expert to ask about this.

Jim

On May 13, 2013, at 11:30 AM, RFoulger wrote:

All the pre-RI literature I've found is Eukaryotic, so I shall
leave that term alone.
should read:
All the pre-IC literature I've found is Eukaryotic, so I shall
leave that term alone.

Other parentage edits I've done:
primosome complex ; GO:1990077
- is_a: protein complex ; GO:0043234
+ is_a: protein-DNA complex ; GO:0032993

DNA replication preinitiation complex ; GO:0031261 (pre-IC)
- is_a: protein complex ; GO:0043234
+ is_a: protein-DNA complex ; GO:0032993

[ontology-requests:#10156]
</p/geneontology/ontology-requests/10156/> definition of primosome

Status: open
Labels: Other term-related request
Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal
Last Updated: Mon May 13, 2013 03:46 PM UTC
Owner: RFoulger

Hi,

I requested a term for the primosome on Friday but now saw that
there are already names in the ontology biological process lineage
that refer to this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they
are entirely parallel in the ontology and don't really differ in
their definition.

Although they refer to eukaryotic replication it looks as if they
could also be applicable to prokaryote replication. In that case
we could call the primosome complex either pre-replicative complex
or replication preinitiation complex. I would probably prefer
pre-replicative complex as then it can also refer to the complexes
formed during restart of replication at a stalled replication fork
(see SF request 3612171)

Thanks,
Birgit

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10156/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054

---

[ontology-requests:#10156]

definition of primosome

Status: open
Labels: Other term-related request
Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal
Last Updated: Mon May 13, 2013 04:30 PM UTC
Owner: RFoulger

Hi,

I requested a term for the primosome on Friday but now saw that there
are already names in the ontology biological process lineage that
refer to this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they are
entirely parallel in the ontology and don't really differ in their
definition.

Although they refer to eukaryotic replication it looks as if they
could also be applicable to prokaryote replication. In that case we
could call the primosome complex either pre-replicative complex or
replication preinitiation complex. I would probably prefer
pre-replicative complex as then it can also refer to the complexes
formed during restart of replication at a stalled replication fork
(see SF request 3612171)

Thanks,
Birgit

---

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/geneontology/ontology-requests/10156/

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--

Dr. Birgit Meldal
IntAct Curator
European Bioinformatics Insitute
Welcome Trust Sanger Centre
Hinxton
Cambridgeshire
CB10 1SD

+44 1223 494107
bmeldal@ebi.ac.uk
http://www.ebi.ac.uk/intact/

[Birgit Meldal]

Could you also please add
is_a GO:0033202 DNA helicase complex

Thanks, Birgit

[RFoulger]

Hi Jim,
Have you had any feedback from your replication colleague? There's a number of terms from Birgit in the TermGenie queue (children of primosome) that I'm keen to add in, which depend on the outcome of the primosome discussion.
Thanks,
Becky

[Jim Hu]

not yet. I will follow up.

Sent from my iPad

On May 22, 2013, at 5:32 AM, "RFoulger" rfoulger@users.sf.net wrote:

Hi Jim,
Have you had any feedback from your replication colleague? There's a number of terms from Birgit in the TermGenie queue (children of primosome) that I'm keen to add in, which depend on the outcome of the primosome discussion.
Thanks,
Becky

[ontology-requests:#10156] definition of primosome

Status: open
Labels: Other term-related request
Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal
Last Updated: Tue May 14, 2013 10:38 AM UTC
Owner: RFoulger

Hi,

I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.

Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)

Thanks,
Birgit

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[Jim Hu]

Hi Rebecca,

Response from Tania Baker at MIT. The reference to her shoulder is that she was injured in a bike accident on the way to the memorial service for the MIT policeman who was killed by the Boston bombers.

Are there followup questions needed?

Jim

Hi Jim:

I did see it---but I haven't had a chance to respond..

I basically agree with your comments "understanding".... although of course not everyone would agree with this (or any) nomenclature call.

I'd go for the "more inclusive"

is that enough help?

(shoulder had a bit of a set back... hurts etc... back on pain meds and imobilization----I may need surgery, but trying to avoid it!)

best,

tania

On May 22, 2013, at 10:21 AM, Jim Hu wrote:

Hi Tania,

Did you see this before?

Jim

Hi Tania,

How is your shoulder? I'm having a discussion with people in the GO consortium about whether these two terms should have eukaryotic in their definitions.

http://gowiki.tamu.edu/wiki/index.php/Category:GO:0071163_!_DNA_replication_preinitiation_complex_assembly

http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006267_!_pre-replicative_complex_assembly

My sense is that the definitions are too narrow. Actually, I think the whole set of terms relating to DNA replication could use an overhaul, but for now my question is whether it is useful to think of the complexes at the origin as analogous.

My understanding is that for both bacteria and eukaryotes the same basic steps happen, but there are differences in the order

Origin recognition - DnaA, lambdaO, ORC
Origin unwinding (not in euks)
Helicase recruitment (DnaB, lambdaP, MCMs)
(additional helicase-dependent unwinding?)
Recruitment of the holoenzyme
Leading strand initiation
Lagging strand initiation
at some point after that we wouldn't think of it as initiation anymore... where would that be?

Thanks!

Best,

Jim

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054

On May 22, 2013, at 5:32 AM, RFoulger wrote:

Hi Jim,
Have you had any feedback from your replication colleague? There's a number of terms from Birgit in the TermGenie queue (children of primosome) that I'm keen to add in, which depend on the outcome of the primosome discussion.
Thanks,
Becky

[ontology-requests:#10156] definition of primosome

Status: open
Labels: Other term-related request
Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal
Last Updated: Tue May 14, 2013 10:38 AM UTC
Owner: RFoulger

Hi,

I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.

Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)

Thanks,
Birgit

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10156/

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=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054

[RFoulger]

Hi Jim,

(just back after the bank holiday).. Thanks for following this up. I'm going to make a taxon-generic term for pre-replicative complex, and make the existing GO:0005656 Eukaryotic-restricted.

I'll expand the pre-IC term (GO:0031261) to make it taxon-generic.

I'm still confused about how the primosome (GO:1990077) fits with the pre-RC and pre-IC complexes (if atall). Could you please ask Tania how they are connected.

Thanks again… and I hope her shoulder injury heals quickly.
Becky

[RFoulger]

These 4 complex terms (submitted by Birgit to TG freeform) may need rehousing under more specific primosome or pre-RC terms, once the primosome/pre-RC terms have been finalised:

DnaB-DnaC complex ; GO:1990100
DnaA-oriC complex ; GO:1990101
DnaA-DiaA complex ; GO:1990102
DnaA-HU complex ; GO:1990103

[RFoulger]

Created new taxon-agnostic pre-RC terms:
pre-replicative complex ; GO:0036387
pre-replicative complex assembly ; GO:0036388

and renamed the existing terms to be Eukaryotic, based on their existing parentage:
pre-replicative complex ; GO:0005656
pre-replicative complex assembly ; GO:0006267

nuclear pre-replicative complex ; GO:0005656
nuclear pre-replicative complex assembly ; GO:0006267

Created new bacterial pre-RC terms:
bacterial pre-replicative complex ; GO:0036389
bacterial pre-replicative complex assembly ; GO:0036390
(discussed in office, and couldn't think of better name that doesn't contain 'bacterial')

STILL TO DO ON THIS TICKET:
! Sort out how primosome fits in with the pre-RC and pre-RI complexes.
! Rehouse Birgits DnaA/DnaB complex terms accordingly (see above)

[Birgit Meldal]

Thanks, Becky :)

On 05/06/2013 17:06, RFoulger wrote:

Created new taxon-agnostic pre-RC terms:
pre-replicative complex ; GO:0036387
pre-replicative complex assembly ; GO:0036388

and renamed the existing terms to be Eukaryotic, based on their
existing parentage:
pre-replicative complex ; GO:0005656
pre-replicative complex assembly ; GO:0006267

nuclear pre-replicative complex ; GO:0005656
nuclear pre-replicative complex assembly ; GO:0006267

Created new bacterial pre-RC terms:
bacterial pre-replicative complex ; GO:0036389
bacterial pre-replicative complex assembly ; GO:0036390
(discussed in office, and couldn't think of better name that doesn't
contain 'bacterial')

STILL TO DO ON THIS TICKET:
! Sort out how primosome fits in with the pre-RC and pre-RI complexes.
! Rehouse Birgits DnaA/DnaB complex terms accordingly (see above)

---

[ontology-requests:#10156]
http://sourceforge.net/p/geneontology/ontology-requests/10156/
definition of primosome

Status: open
Labels: Other term-related request
Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal
Last Updated: Mon Jun 03, 2013 04:17 PM UTC
Owner: RFoulger

Hi,

I requested a term for the primosome on Friday but now saw that there
are already names in the ontology biological process lineage that
refer to this complex in eukaryotes:

GO:0071163 DNA replication preinitiation complex assembly, and
GO:0006267 pre-replicative complex assembly.

I'm struggling to see the difference between these two terms, they are
entirely parallel in the ontology and don't really differ in their
definition.

Although they refer to eukaryotic replication it looks as if they
could also be applicable to prokaryote replication. In that case we
could call the primosome complex either pre-replicative complex or
replication preinitiation complex. I would probably prefer
pre-replicative complex as then it can also refer to the complexes
formed during restart of replication at a stalled replication fork
(see SF request 3612171)

Thanks,
Birgit

---

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https://sourceforge.net/p/geneontology/ontology-requests/10156/

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--

Dr. Birgit Meldal
IntAct Curator
European Bioinformatics Insitute
Welcome Trust Sanger Centre
Hinxton
Cambridgeshire
CB10 1SD

+44 1223 494107
bmeldal@ebi.ac.uk
http://www.ebi.ac.uk/intact/