PMID: 25888589 A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors

[CuzickA]

For curation by @smvelasquez

[jseager7]

has there been any progress on following up whether this can be done automatically for any existing annotations using this AE?

@CuzickA I think there is a script to do this automatically but I haven't had time to test it locally, sorry. If this is a problem for other unapproved sessions then I'll work on it as soon as I have some free time.

[CuzickA]

has there been any progress on following up whether this can be done automatically for any existing annotations using this AE?

@CuzickA I think there is a script to do this automatically but I haven't had time to test it locally, sorry. If this is a problem for other unapproved sessions then I'll work on it as soon as I have some free time.

Thanks @jseager7. I guess I was thinking more of whether we needed to update the approved sessions. What happens when a config change is made in PHI-Canto - do changes filter though to all the approved annotations or will we have a mixed set of information on the PHI5 website depending on when the session was curated?

[CuzickA]

Did anyone respond at all? Definitely re-send it shouldn't take this long, but it could have fallen between releases. @Antonialock when was the last UniProt release?

Only the initial automated response providing the #help numbers (documented above in this ticket).

[jseager7]

What happens when a config change is made in PHI-Canto - do changes filter though to all the approved annotations or will we have a mixed set of information on the PHI5 website depending on when the session was curated?

Not sure yet. I'll have to test on a copy of the production server's sessions.

[smvelasquez]

@CuzickA Hi Alayne, I was looking at the new PHIPO terms suggestions, and I think they are ok. Just one thing, would it make sense to add an AE about what proteins are doing the phosphorylation of SGT1, or is that unnecessary information? Because MEK2DD phosphorylates SIPK who in turn phosphorylates SGT1.

[CuzickA]

Hi @smvelasquez, thank you for checking the PHIPO terms in https://github.com/PHI-base/phipo/issues/376.

I'm not sure that we can cover all the detail of 'MEK2DD phosphorylates SIPK who in turn phosphorylates SGT1' in AEs.

I thought I'd add the second sentence here to the definition to cover these cases 'presence of host protein phosphorylation with pathogen' A pathogen host interaction phenotype in which the phosphorylation of one or more specific host proteins, or of specific host protein sites, occurs during pathogen infection (GO:0006468 protein phosphorylation). Either the pathogen or the host could be responsible for the host protein phosphorylation.

Also we have these annotations

Do you think this enough? @ValWood any thoughts?

[ValWood]

If they did the assays this is really useful information to also capture using GO.

Like this: https://www.pombase.org/gene/SPAC24B11.11c We really like to capture 'targt' proteins with GO.

The required_for is incorrect: indicates that a modification is required for a GO function or process

I don't think this particular qualifier is used often but it is related to the gene being modified, not to the modifier. I will try to find an example of usage. You don't need to specify that MEK2 is a protein kinase in the modification annotation, because it's implicit for any phosphorylation adding modifier.

[ValWood]

Re required_for only 16/ 60246 modification at PomBAse use this relation extension. I don't think we really need to capture the 'required for' here, as the most current way to do this is to use GO annotation and attach the GO annotation to the 'modified entity'. I think we will probably remove this qualifier and reannotate these (otherwise i is unnecessary redundancy, and not sustainable to capture all GO dependencies on modified forms). If you are interested here is an example of how we would represent the which modified form is required for an process, or activity

https://www.pombase.org/gene/SPBC244.01c (see the molecular function section). We request the modified forms from PRO https://lod.proconsortium.org/yasgui.html Since GO is a bit of a side annotation for you, you probably don't want to bother with the modified forms.

[ValWood]

"Either the pathogen or the host could be responsible for the host protein phosphorylation."

Is that true. Do pathogens secrete "protein kinase effectors"

[ValWood]

Hang on. For the modification Zea Mays with tobacco MAP kinase Kinase.

I think you can record the phosphorylation site, but the modifications should report physiologically relevant information for the species. So we can't capture the assayed using as an extension from a different species (even though it would almost certainly translate to the Zea. Mays system). If you want to capture this, you could request a species agnostic ID for this protein from PRO, but I would maybe skip it at this stage.

[ValWood]

For the uniprot inquiry I would resend the original helpdesk e-mail since that will ping the helpdesk and the person assigned to the ticket.

[Antonialock]

A0A0D1C8C8 is still in trembl in the internal database so it doesn't look like anyone has updated it. I don't see our helpdesk sorry.

[CuzickA]

Thanks. I've just resent the original UniProt emails back to the Helpdesk for follow up.

[CuzickA]

"Either the pathogen or the host could be responsible for the host protein phosphorylation."

Is that true. Do pathogens secrete "protein kinase effectors"

Hmmm... Good spot. I've been looking for examples but so far have not come up with a good one. I was thinking of this example but its not the pathogen effector avrB directly phosphorylating host RIN4. 'AvrB-induced RIN4 phosphorylation depends on host RIPK.'

I will remove the sentence above for now and it can be added back in the future if we curate an appropriate example.

[CuzickA]

So for the Protein modifications we have

tobacco MEK2 phosphorylating tobacco SIPK

tobacco SIPK phosphorylating maize SGT1 @ValWood, are you suggesting that I need to remove the AE 'added_by Q9M6Q9_TOBAC' as this comes from a different species?

Now updated 15_11_22

[CuzickA]

As a general rule should we NOT be adding AE information for genes/proteins from species different than the primary annotation?

Apart from 'Physical interactions' where this has been adapted to accommodate two species.

[CuzickA]

If the above is the case then this first GO MF annotation will probably need AE 'has_input 100282745' (Maize SGT1) removing.

_Now updated 15_1122

[ValWood]

Maybe you can do this for phenotypes, as it is capturing the experiment. For GO the species must match.

[CuzickA]

Still left to do for this ticket

1. Wait for UniProt gene names to be updated.
2. Make PHIPO release and update terms in annotations. _DONE 23_1122
3. Request new GO BP terms. Terms requested, ticket link below. (4. @jseager7 was going to test if config changes in PHI-Canto filter though to all the approved annotations.) _Now done 25_1122, see comment below. _5. Request AE 'assayedusing' for new phosphorylation PHIPO terms. request made here https://github.com/PHI-base/config/issues/62

[CuzickA]

@ValWood It looks like we may need some new GO BP terms

Is this something that you could follow up or perhaps point me in the right direction to make the NTRs please?

[ValWood]

Could you list he term requests here, I can check that they sound OK, and then we can request them? The pathogen host branch of GO is changing a lot....I am not so involved in this GO sub-project now.

[CuzickA]

Thanks @ValWood

Proposed parent term 'GO:0140418 effector-mediated modulation of host process by symbiont' A process mediated by a molecule secreted by a symbiont that results in the modulation (either activation or suppresion) of a host structure or process. The host is defined as the larger of the organisms involved in a symbiotic interaction. PMID:21467214

Just noticed a typo in above... should be 'suppression' not 'suppresion'. (also a typo in GO:0140590 'supression' should be 'suppression').

NTR: effector-mediated modulation of host DNA synthesis by symbiont A process mediated by a molecule secreted by a symbiont that results in the modulation (either activation or suppression) of DNA synthesis involved in DNA replication (GO:0090592). The host is defined as the larger of the organisms involved in a symbiotic interaction. PMID:25888589

AND child term NTR: effector-mediated induction of host DNA synthesis A process mediated by a molecule secreted by a symbiont that results in the activation of DNA synthesis involved in DNA replication (GO:0090592). The host is defined as the larger of the organisms involved in a symbiotic interaction. PMID:25888589

Here is the text from the publication "See1 Is Required for U. maydis-Induced Plant DNA Synthesis during Leaf Tumor Formation Because see1 expression is prominent during tumor enlargement and our initial observations indicated that SG200Δsee1 hyphae were mainly restricted within mesophyll and bundle-sheath cells, we performed a more thorough confocal microscopy investigation of leaf infections. U. maydis-induced tumor growth reflects host proliferation, then cell expansion; thus, DNA synthesis is a prerequisite for growth. To monitor DNA synthesis in planta, we treated uninfected and infected leaves with 5-ethynyl-2-deoxyuridine (EdU) at several time points over a period of 5 h and then harvested samples. Incorporation of EdU was visualized by attaching a fluorescent tag (AF-488). Maize nuclei were stained with propidium iodide (PI) following a procedure described previously for maize anthers (Kelliher and Walbot, 2011). In maize leaves at 2 DPI, EdU treatment did not result in any detectable labeling. We observed this in maize leaves colonized with U. maydis and in uninfected maize leaves (Figure 3A), suggesting that no or only rare, sporadic maize DNA synthesis occurs in seedling leaf blades during the early phase of infection. We conclude that in the infected zones, the host cells were already postmitotic. By 4 DPI, when the first macroscopic symptoms appear in wild-type infections, EdU incorporation into leaf DNA was widespread (Figure 3A). Leaf cells invaded by fungal hyphae synthesized new DNA, and this coincided with the induction of mitosis, which could be visualized at different stages of cell division and as contiguous pairs of similarly labeled cells (Figure 3B). Such invaded cells also underwent multiple division events over several days (Figure 3B)."

[ValWood]

This sounds OK, or at least close enough that Pascale will be able to advise how they are modelling these types of process (I haven't been attending the ontology calls for multispecies so I lost track about recent changes) Can you request it here: https://github.com/geneontology/go-ontology

[CuzickA]

Thanks, just done that here https://github.com/geneontology/go-ontology/issues/24370

[CuzickA]

Summary of curation issues and tips to document from this session (that have not already been covered in https://github.com/PHI-base/curation/issues/104)

1) Only use one time point in the conditions from PHI-ECO per annotation. 2) Make it clear when to make a 'Wild-type RNA level' annotation vs a phenotype annotation. 3) How to use the allele type 'transformant'. 4) GO primary annotation species must be the same as AE assayed_using species. https://github.com/PHI-base/curation/issues/111

I've made a note to include above in curation tips / FAQ document in https://github.com/PHI-base/canto-docs/issues/10

[CuzickA]

Hi @ValWood if the new suggested GO BP term "effector-mediated induction of cell cycle reactivation in host" is created, do you think that these types of PHI phenotype annotations are still okay?

The publication results subheading is 'See1 Is Required for U. maydis-Induced Plant DNA Synthesis during Leaf Tumor Formation' so the text mentions host DNA synthesis.

[jseager7]

@CuzickA Just to note, I've renamed has_substrate to has_input in all curation sessions now. The script affected an approved session so it seems to apply to all sessions regardless of status.

[ValWood]

The phenotypes are OK. This was what is observed, alterations to replication.

What seems to be happening is that the cells are forced to re-enter the cell cycle more quicky than they would for normal growth/maintenance. DNA synthesis is used as the 'indicator' for cell cycle activation ( SGT1 it's presumed effector is not closely connected to DNA synthesis, It seems to actually be part of a signalling pathway that halts the cell cycle in fission yeast). So, for the process" induction of the cell cycle" is what is happening. They could have monitored other cell cycle events (actually they don't even seem to assay replciation directly).

"Required for" is always a clue. "Required for" is often used when some gene is needed upstream of another event. For example, DNA replication is 'required for chromosome segregation' but it isn't involved in chromosome segregation it is upstream. Similarly here "reactivation of the cell cycle" (proposed to involve SGT1) is "required for DNA replication.

In the longer term, when you know what pathways the pathogens target you might want to reduce the scope of PHIPO and model these pathogen host interactions as phenotypes of the cell cycle re-entry and put the details in the assay using ECO terms.

This one is a bit tricky though, the authors don't to assay DNA replication specifically, it seems they chose that process because they saw a lot of replciation-associated genes were upregulated. In reality you don't just "activate DNA replication" the cells need to make appropriate cell cycle transitions to proliferate G1-S/ G2-M/M-G1 to grow and divide, so the effector is regulating more than "replication" it is pushing the cells into S-phase.

A useful tip is to notice when researcher say "required for" because usually, this means you need to be very careful about the GO process you associate with. GO is about the evolved role. The goal here is to reactivate the cell cycle.

Interestingly SGT1 isn't very well characterise any yeast species, but DNA replication s well enough characterised that it could only likely operate before the G1/S transition.

[CuzickA]

Thanks @ValWood, that's really helpful :-).

[CuzickA]

AE assayed_using now added.

Approving session. Keeping ticket open as still waiting on new GO term and UniProt gene name updates.

[CuzickA]

New GO term now added

Still waiting for UniProt gene name updates for [help #222200] [uuw] UniProtKB/TrEMBL B4FQV3 entry update request [help #222201] [uuw] UniProtKB/TrEMBL Q9M6Q9 entry update request Original emails sent 16 May 2022 Follow up email sent 11 Nov 2022 Further follow email sent today 10 May 2023

This one has been done [help #222199] [uuw] UniProtKB/TrEMBL A0A0D1C8C8 entry update request

UMAG_02239 has now changed to See1

[Antonialock]

What do you need from UniProt (I can't see our helpdesk tickets)?

On Wed, May 10, 2023 at 3:12 PM Alayne Cuzick @.***> wrote:

New GO term now added [image: image] https://user-images.githubusercontent.com/11753634/237413261-e455f927-5ba7-4877-b4a1-0200e5d85f9a.png

Still waiting for UniProt gene name updates for [help #222200] [uuw] UniProtKB/TrEMBL B4FQV3 entry update request [help #222201] [uuw] UniProtKB/TrEMBL Q9M6Q9 entry update request Original emails sent 16 May 2022 Follow up email sent 11 Nov 2022 Further follow email sent today 10 May 2023

This one has been done [help #222199] [uuw] UniProtKB/TrEMBL A0A0D1C8C8 entry update request [image: image] https://user-images.githubusercontent.com/11753634/237415634-86fa15d7-490d-4fcf-ae64-3ef0246b0b1c.png

UMAG_02239 has now changed to See1

— Reply to this email directly, view it on GitHub https://github.com/PHI-base/curation/issues/103#issuecomment-1542287246, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBDJUSOH24LJ7IGU6VJPPDXFOO3JANCNFSM5SBRDDVQ . You are receiving this because you were mentioned.Message ID: @.***>

[CuzickA]

Hi @Antonialock :-)

Here is a copy of the emails requesting gene name updates

[help #222200] [uuw] UniProtKB/TrEMBL B4FQV3 entry update request

[help #222201] [uuw] UniProtKB/TrEMBL Q9M6Q9 entry update request

We load the 'gene name' into PHI-Canto.