Should GO:0019035 'viral integration complex' definition changed to reflect the new restriction 'Never Vertebrata' (or obsoleted)?

[pgarmiri]

Hi,

The definition of the term GO:0019035 'viral integration complex' states that it contains host proteins.

Definition (GO:0019035 GONUTS page)

A nucleoprotein complex containing viral genetic material and associated viral and host proteins, which is capable of inserting a viral genome into a host genome. PMID:16712776

There are two human proteins affected (TOP2A (P11388) and TOP2A (Q02880)). The annotations are based on the publication cited in the definition and I am deleting them.

As this is a hijacked function of the protein it might be confusing as a stand-alone annotation for the human proteins. Perhaps the term should be obsoleted or include a note that it should not used with the human participants?

Thanks, Penelope

[pgarmiri]

Another term that gives an error :

GO:0020005 'symbiont-containing vacuole membrane'

Definition (GO:0020005 GONUTS page)

The lipid bilayer surrounding a symbiont-containing vacuole, derived from both the host and symbiont.

68 annotations

GO:0020005 JSON symbiont-containing vacuole membrane

Cellular Component Definition (GO:0020005 GONUTS page)

Example of use: In PMID: 23245326, they investigate the human platelet factor 4 (hPF4) and found that it kills malaria parasites inside erythrocytes by selectively lysing the parasite digestive vacuole (DV). and PMID:18665841 They found that found that Aquaporin‐1 (AQP1), a water channel that regulates swelling of secretory vesicles, associated with PCV (pathogen‐containing vacuoles). AQP1 controls membrane integrity in response to bacterially induced membrane damage.

A moonlighting protein it seems.

[ValWood]

The term "symbiont containing vacuole" under "host cell part" does not make sense form a GO perspective

The symbiont containing vacuole is a host digestive vacuole, and if a pathogen protein is located there that isn't it's place of action, it is being digested.

If annotating a human protein "lytic vacuole" would be correct term probably?, or is a specific "symbiont-containing vacuole" term is required, this term should move there, it should not be in the "host cell part" branch.

[pgarmiri]

There is a note in the definition of "symbiont containing vacuole" that explains why this can't be linked to 'vacuole' or it's children (see below)...So, I suppose we need a seperate term.

Note that this term does not have a relationship to 'vacuole ; GO:0005773' because it does not fit the definition of a vacuole; the parasitophorous vacuole was so named because it resembles a vacuole in the microscope.

Any thoughts on where this term (and the child terms) could be moved under?

[pgaudet]

@dsiegele @mgiglio99 Thoughts ?

[ValWood]

The 2 publications above seem to refer to. 2 different things.

1. PMID: 23245326 seems to be describing https://en.wikipedia.org/wiki/Parasitophorous_vacuole#:~:text=The%20parasitophorous%20vacuole%20(PV)%20is,contains%20cytoplasm%20and%20the%20parasite. The parasitophorous vacuole (PV) is a structure produced by apicomplexan parasites in the cells of its host. The PV allows the parasite to develop while protected from the phagolysosomes of the host cell. The PV is a bubble-like compartment made of plasma membrane; the compartment contains cytoplasm and the parasite.

2. PMID:18665841 seems to describing a host vacuole which is used to compartmentalize bacteria

That's what it looks like, although I'm not familiar with this.... But if so we need to be sure it is clear which is which and be clear about what would be annotated to these terms.

I would not annotate a host protein to anything describing (1) unless it enters the vacuole (and in this case we have not encountered this type of host protein inside pathogen yet and may need its own branch). I don't really know what would be annotated to (1) on a gene product basis because the term would seem to be for the pathogen/symbiont, but the entirety of the symbiont(s) is/are within the "Parasitophorous vacuole".

anyway it seems that we are conflating two structures,....

[pgarmiri]

In case (1) it seems that it does actually enter the vacuole. Fig 1

Parasites were assayed for both hPF4 localization using immunofluorescence analysis (IFA) and direct GFP signal (integrity of the DV; Figure 1D). Within 1 min of hPF4 incubation, hPF4 staining could be detected in the cytoplasm of only infected erythrocytes. hPF4 continued to accumulate over the next several minutes, wherein it entered the parasite cytoplasm and colocalized with the parasite DV. Next, severe perturbation of the DV allowed GFP to diffuse throughout the parasite cytoplasm (Figure 1D, Figures S1A and S1B). Western blot analysis of hPF4 confirmed the IFA results showing entry into erythrocytes by 1 min followed by accumulation into the parasite within 5 min (Figure 1E).

In case (2) the human protein has been annotated with GO:0085018 JSON maintenance of symbiont-containing vacuole by host

Biological Process Definition (GO:0085018 GONUTS page)

The process in which a host organism maintains the structure and function of a symbiont-containing vacuole. The symbiont-containing vacuole is a membrane-bounded vacuole within a host cell in which a symbiont organism resides, and can serve to reduce pathogenicity of invading symbionts by restricting them to the vacuolar compartment. PMID:18665841 (the actual paper referred above)

This function is only during response to bacterial infection/defense response. It could be added as an extension or as a note?

[pgarmiri]

Hello, Any further thoughts on this? Thanks, Penelope

[pgarmiri]

@pgaudet , When @mgiglio99 talked about host symbiont vacuoles, I remembered I had opened a relevant ticket a while ago... I just managed to locate it and thought to bring it to your attention. :) Thanks, Penelope

[pgaudet]

~Discussion on the multiorg call:~ ~* GO:0019035 'viral integration complex' we propose to change the definition from "A nucleoprotein complex containing viral genetic material and (~associated viral and host proteins, which is~) capable of inserting a viral genome into a host genome" to "A nucleoprotein complex containing viral genetic material capable of inserting a viral genome into a host genome."~

~And add a taxon restriction, only in viruses.~

[pgaudet]

• [ ] After further investigation, the decision is to obsolete "GO:0019035 'viral integration complex' " - it looks like from the viral part it's only the integrase that plays an active role in the process. Host proteins participate but do not form a 'stable complex' in the GO-sense. See Fig 1 in PMID:17320002

[dsiegele]

@pgaudet I did some additional research on viral integration complexes. Based on the following references, I think we should reconsider obsoleting the GO term GO:0019035 'viral integration complex'.

In infected cells, retroviruses form a stable nucleoprotein complex called the pre-integration complex or intasome, which can be isolated from infected cells and stays intact through gel filtration and equilibrium density centrifugation. The composition of the PIC seems to depend on how it is isolated and how far along it is in the process of maturation. See Figure 1 in Scoca and Di Nunzio. The PIC always contains the viral DNA and the viral Integrase protein. Other viral proteins that may be associated with the PIC are multimers of the capsid protein, which are needed for transport into the nucleus.

• Scoca V, Di Nunzio F. (2021) The HIV-1 Capsid: From Structural Component to Key Factor for Host Nuclear Invasion. Viruses 13(2):273. doi: 10.3390/v13020273. PMID: 33578999 PMCID: PMC7916756 (Free PMC article)

• Paul Lesbats, Alan N Engelman, Peter Cherepanov (2016) Retroviral DNA integration . Chem Rev 116(20):12730-12757. doi: 10.1021/acs.chemrev.6b00125. PMID: 27198982 PMCID: PMC5084067 (Free PMC article)

"Replication via formation of a stable DNA form makes retroviruses particularly amenable to reverse genetics. Accordingly, functions of retroviral gene products have been extensively probed through mutagenesis. In early studies, IN was identified as the protein product encoded within the 3′ portion of the retroviral pol gene that was essential for efficient retroviral replication and integration (8−11). Reverse transcription of the diploid retroviral RNA genome results in the formation of a linear double-stranded viral DNA (vDNA) molecule carrying a copy of the long terminal repeat (LTR) sequence at either end (12−15). The vDNA molecule exists in the form of a preintegration complex (PIC) (16,17) that is rather poorly biophysically characterized due to the scarce level at which it forms, ca. one copy per cell, during acute virus infection. Nevertheless, PICs have been reported to contain a number of cellular and viral proteins, most notably IN (18−26). Once the PIC gains access to the nuclear compartment, the vDNA ends are inserted into a cellular chromosome. This step, initiated by the enzymatic action of IN and completed by the host cell DNA repair machinery, is a point of no return: the cell becomes a permanent carrier of the integrated viral genome, which is referred to as the provirus.

• Robert Craigie (2018) Nucleoprotein Intermediates in HIV-1 DNA Integration: Structure and Function of HIV-1 Intasomes. Subcell Biochem 88:189-210. doi: 10.1007/978-981-10-8456-0_9. PMID: 29900498 PMCID: PMC6370045 (Free PMC article)

• S Q Wei, K Mizuuchi, R Craigie (1997) A large nucleoprotein assembly at the ends of the viral DNA mediates retroviral DNA integration. EMBO J 16(24):7511-20. doi: 10.1093/emboj/16.24.7511. PMID: 9405379 PMCID: PMC1170350 (Free PMC article)

• B Bowerman, P O Brown, J M Bishop, H E Varmus (1989) A nucleoprotein complex mediates the integration of retroviral DNA. Genes Dev 3(4):469-78. doi: 10.1101/gad.3.4.469. (Free Article) PMID: 2721960

[pgaudet]

from @genegodbold

https://pubmed.ncbi.nlm.nih.gov/21037296/ Nuclear targeting of a bacterial integrase that mediates site-specific recombination between bacterial and human target sequences

There are only four papers found in a search for “bacterial integrase” on PubMed https://pubmed.ncbi.nlm.nih.gov/?term=%22bacterial+integrase%22%5Btiab%5D&sort=date&size=200

[pgaudet]

Hi @dsiegele Thanks for digging those out! I am not quite sure how to describe the complex from these - the first paper does not characterize the components of the complex, and the second describes the integrase and its substrate (?)

For now:

• [x] changed the definition from from "A nucleoprotein complex containing viral genetic material and associated viral and host proteins, which is capable of inserting a viral genome into a host genome." to: "A nucleoprotein complex containing viral genetic material and the viral integrase, required for genome integration into the host's genome. May contain other proteins."
• [x] ~added taxon restrictions: never in eukaryotes and never in archae (so that the term is allowed in viruses and bacteria)~
• [ ] added taxon restriction to 'only in viruses'
• [x] changed subclass from part_of GO:0042025 ! host cell nucleus to part_of GO:0043657 ! host cell (to allows annotation of phages)
• [x] Updated references - removed PMID:16712776 (that @pgarmiri reported as incorrect), to add the references cited by @genegodbold and @dsiegele , PMID:21037296, PMID:2721960, PMID:29900498

Thanks, Pascale

[pgarmiri]

Another term that gives an error :

GO:0020005 'symbiont-containing vacuole membrane'

Definition (GO:0020005 GONUTS page)

The lipid bilayer surrounding a symbiont-containing vacuole, derived from both the host and symbiont.

68 annotations

GO:0020005 JSON symbiont-containing vacuole membrane

Cellular Component Definition (GO:0020005 GONUTS page)

Example of use: In PMID: 23245326, they investigate the human platelet factor 4 (hPF4) and found that it kills malaria parasites inside erythrocytes by selectively lysing the parasite digestive vacuole (DV). and PMID:18665841 They found that found that Aquaporin‐1 (AQP1), a water channel that regulates swelling of secretory vesicles, associated with PCV (pathogen‐containing vacuoles). AQP1 controls membrane integrity in response to bacterially induced membrane damage.

A moonlighting protein it seems.

Any thoughts on this term?

[genegodbold]

@pgarmiri @pgaudet I'm not sure about the "derived from symbiont" part. I don't think intracellular pathogenic bacteria regularly donate their lipids to these vacuoles (for instance), but they do bring about changes in the host cell to make these things. Those changes typically involve at least one of three things: (1) manipulation of host small GTPases--this can sometimes (but not always) lead to (2) manipulation of the host cytoskeleton AND/OR (3) manipulation of the host endomembrane system.

[pgaudet]

On the multiorganism call: propose to remove the parent ' GO:0065010 extracellular membrane-bounded organelle', since this is not an organelle, and this makes the term a child of both 'host part' and of the 'normal' cellular components.

[pgarmiri]

Thank you @genegodbold @pgaudet !

Perhaps a change in the wording of the definition or a note could clarify this term and its usage.

I notice that these two terms, GO:0020003 'symbiont-containing vacuole' and GO:0020005 'symbiont-containing vacuole membrane'

don't allow annotation to mouse and human proteins as they both have the following Taxon Constrain.

Taxon Constraints

The use of this term should conform to the following taxon constraints:

Ancestor GO ID | Ancestor GO Term Name | Relationship | Taxon ID | Taxon | Reference(s) -- | -- | -- | -- | -- | -- GO:0033643 | host cell part | Never in Taxon | 7742 | Vertebrata |  

Definition (GO:0033643)

Any constituent part of a host cell. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Vertebrates are often the host, so is this constrain valid? Or is it meant only for proteins of organisms that interact with a host?

If there is an issue that would affect all the terms that are linked to 'Host cell part'.

Thanks, Penelope

[pgarmiri]

To clarify my point: If GO:0020003 'symbiont-containing vacuole' and GO:0020005 'symbiont-containing vacuole membrane' are be used for host proteins only being under GO:0033643 'host cell part' will prevent this due the taxon constrain.

[genegodbold]

Hey @pgarmiri, we talked about this with @pgaudet on this week's multiorganism call. Did we resolve anything? Here are the notes: "not yet resolved for 'symbiont-containing vacuole (membrane)' - annotations: https://docs.google.com/spreadsheets/d/1GJ1wvQ8Z9qi7dTjWwdVTPB6QZ3WFbJYHlQ1jYOgCSEw/edit#gid=0"

[mgiglio99]

If I recall, I think we concluded that host proteins that end up being in the 'symbiont-containing vacuole membrane' have been hijacked. But we didn't decide what to annotate them with in place of the symbiont vacuole membrane term. Should they get only whatever component annotations they would have if there was no symbiont around?

[pgaudet]

Did we say that the 'symbiont-containing vacuole' was a host CC or a symbiont CC? I thought we decided it was a host CC.

[genegodbold]

@pgaudet, What is "CC"? It should be a host entity in terms of the majority of its composition, but it has been hijacked by the symbiont. To make a probably bad, and perhaps dangerous, computer analogy: the code is still mostly the host, but a few hacking insertions have put it under the control of the symbiont.

[pgaudet]

@genegodbold CC is the cellular component part of the ontology - sorry about the jargon ;)

I was asking because this term is unusually represented as being part of both the host and the symbiont

This drives which genes can be annotated to it. I think @mgiglio99 suggested we remove the extracelluar parent (this structure is extracellular relative to the symbiont). Since its a child of 'host cell cytoplasm part', only symbiont proteins should be annotated.

We can create a counterpart 'symbiont-containing vacuole' for annotating host proteins if this is relevant.

Thoughts?

[genegodbold]

@pgaudet My initial thought is "This is hard" But if there should be a list of terms peculiar to symbiont-host biology, then the parasitophorous vacuole (PV), however it is designated, should definitely be one of them.

[Antonialock]

Note to self:

Curator Constraint Entity Type Entity ID GO ID Name Evidence Reference Taxon ID Taxon Name Yasmin Alam-Faruque [Expired acc...GO:0033643 never_in_taxon Vertebrata protein P29972 GO:0020003 symbiont-containing vacuole ECO:0000250 (ISS) GO_REF:0000024 9606 Homo sapiens Yasmin Alam-Faruque [Expired acc...GO:0033643 never_in_taxon Vertebrata protein P29972 GO:0020005 symbiont-containing vacuole membrane ECO:0000314 (IDA) PMID:18665841 9606 Homo sapiens Yasmin Alam-Faruque [Expired acc...GO:0033643 never_in_taxon Vertebrata protein Q02013 GO:0020003 symbiont-containing vacuole ECO:0000314 (IDA) PMID:18665841 10090 Mus musculus Michele Magrane GO:0033643 never_in_taxon Vertebrata protein Q9QZ85 GO:0020005 symbiont-containing vacuole membrane ECO:0000314 (IDA) PMID:18772884 10090 Mus musculus

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