PMID:19900007 Mutations in a beta-tubulin confer resistance of Gibberella zeae to benzimidazole fungicides

[MPiovesana]

Curated by @MPiovesana https://canto.phi-base.org/curs/61b19e1cc3d55d37

[MPiovesana]

Natural isolates of Gibberella zeae with susceptible or moderate/high resistance to carbendazim are described in this paper. The sequence of the β-tubulin gene of these strains was analysed and point mutations were identified. Deletion and complementation lines were generated to confirm the link between β-tubulin alleles and chemical resistance phenotypes. NOTE: I think the curation of this paper is a little tricky as ideally we would need to add 3 Uniprot IDs, one for the β-tubulin sequence of each mutant. Below I explained my rationale for the curation so far, but perhaps it needs to be discussedl.

[MPiovesana]

Uniprot ID: searching the reference proteome of G. zeae in Uniprot, entry Q4HZS8 was retrieved for β-tubulin.

Strains: strains 2021 (sensitive), R9 (moderately resistant) and JT04 (highly resistant) were added to this curation session.

[MPiovesana]

Genotype creation: deletion lines of all three strains were recorded as βTubΔ. The complementation lines were recorded as transformant alleles with βTubΔ as background:

βTub transformant(R9-βTub(F167Y)): βTub from strain R9 harbouring aaF167Y (inserted in 2021)

βTub transformant(JT04-βTub(G73R Q198L)): βTub from strain JT04 harbouring aaG73A Q198L (inserted in 2021)

βTub transformant(2021-βTub(Y167F)): βTub from strain 2021 harbouring aaY167F (inserted in R9)

βTub tranformant(2021-βTub(R73G L198Q): βTub from strain 2021 harbouring aaR73G L198Q (inserted in JT04)

Transformant alleles were assigned ectopic expression level.

[MPiovesana]

Genotype annotations: genotypes were annotated with PHIPO terms "sensitive / resistance to carbendazim" as appropriate.

[MPiovesana]

Curation completed pending review.

[CuzickA]

NOTE: I think the curation of this paper is a little tricky as ideally we would need to add 3 Uniprot IDs, one for the β-tubulin sequence of each mutant. Below I explained my rationale for the curation so far, but perhaps it needs to be discussedl.

I think this UniProt query relates to the fact that we cannot curate the natural sequence variation in the following

Strains: strains 2021 (sensitive), R9 (moderately resistant) and JT04 (highly resistant)

and the reference UniProt sequence may also be different.

This is an issue we are aware of. In the future we may try to enable an option in PHI-Canto to load individual sequences, but this is not possible at the moment.

[CuzickA]

I think there may be an issue with the AA alterations here

In the Table

It looks like the changes between strain 2021 and JT04 should be Q73R, E198L . @MPiovesana please could you double check this for me? Or have I misread something?

[MPiovesana]

It looks like the changes between strain 2021 and JT04 should be Q73R, E198L . @MPiovesana please could you double check this for me? Or have I misread something?

@CuzickA Yes indeed, I can see now that I made a mistake with the one-letter code for these residues, apologies for that! Depending on the direction of the genetic transfer (2021 to JT04 or JT04 to 2021), the alleles should read:

βTub transformant(JT04-βTub(Q73R E198L)): βTub from strain JT04 harbouring aaQ73A E198L (inserted in 2021)

βTub tranformant(2021-βTub(R73Q L198E): βTub from strain 2021 harbouring aaR73Q L198E (inserted in JT04)

[CuzickA]

Thanks for double checking @MPiovesana. I'll make the changes as I check the session :-)

[MPiovesana]

@CuzickA thank you very much and apologies for the confusion again!

[CuzickA]

Now looks like this

Note: AE alteration to archetype only add to the annotations where the direction of change is a shift towards resistance.

Approving session and closing ticket

[CuzickA]

AE alteration_in _archetype

F167Y; β-tubulin; ASPEND Q73R, E198L; β-tubulin; ASPEND

Straight forward to find in Nichola's S file in Table S1

Question Same question about double mutants as in https://github.com/PHI-base/curation/issues/144

[CuzickA]

Same question about double mutants as in https://github.com/PHI-base/curation/issues/144 This is ok

[CuzickA]

AE alteration_in _archetype checked by Nichola. Session now approved.