SPKWs for Sc TOS4, TOS8, & PLM2

[gocentral]

Hi,

Please check on the associated keywords for TOS4, TOS8, & PLM2 from S. cerevisiae:

• KW-0238 (DNA binding)
• KW-0805 (Transcription regulation)
• KW-0804 (Transcription)

While Horak et al. 2002 (PMID: 12464632) stated that these proteins are transcription factors, I have just reviewed the literature and do not see any evidence showing this. The Horak paper shows chromatin association but does not conclusively show that any of these three proteins binds DNA directly or is involved in transcription or transcriptional regulation.

thanks,

-Karen

Reported by: krchristie

Original Ticket: "geneontology/annotation-issues/675":https://sourceforge.net/p/geneontology/annotation-issues/675

[gocentral]

• assigned_to: nobody --> edimmer

Original comment by: mah11

[gocentral]

HI Karen,

I appear to have some mappings to transcription related terms for TOS4 from SGD. I will remove these but the SGD description is Transcription factor that binds to a number of promoter regions, particularly promoters of some genes involved in pheromone response and cell cycle; can you confirm that this is now incoorrect before I remove my annotations

Thanks

Val

Original comment by: ValWood

[gocentral]

In pombe Tos4 has name has recently been reserved by Jurg Bahler with "similar to S. cerevisiae tos4, and seems to have related roles in controlling cell cycle-regulated transcription" so I think the TOs4 (and paralogous PLM2) mappings to transcription/regulation are probably OK)

Also TOS8 is a homeobox protein, so here DNA binding at least seems to be a reasonable inference.

Val

Original comment by: ValWood

[gocentral]

HI Karen,

I appear to have some mappings to transcription related terms for TOS4 from SGD. I will remove these but the SGD description is Transcription factor that binds to a number of promoter regions, particularly promoters of some genes involved in pheromone response and cell cycle; can you confirm that this is now incoorrect before I remove my annotations

Thanks

Val

Original comment by: ValWood

[gocentral]

Hi Val,

For reasons related to our upcoming transition to new hardware, I have not yet updated the descriptions for any of these three genes. The new ones will be these:

TOS8 - Homeodomain-containing protein and putative transcription factor found associated with chromatin; target of SBF transcription factor; induced during meiosis and under cell-damaging conditions; similar to Cup9p transcription factor

ref: Horak et al. 2002 PMID: 12464632

---

PLM2 - Forkhead Associated domain containing protein and putative transcription factor found associated with chromatin; target of SBF transcription factor; induced in response to DNA damaging agents and deletion of telomerase; similar to TOS4

Huang M, Elledge SJ. (2000) PMID: 12760057 Nautiyal S, et al. (2002) PMID: 12084816 Horak et al. 2002 PMID: 12464632

---

TOS4 - Forkhead Associated domain containing protein and putative transcription factor found associated with chromatin; target of SBF transcription factor; expression is periodic and peaks in G1; similar to PLM2

Huang M, Elledge SJ. (2000) PMID: 12760057 Horak et al. 2002 PMID: 12464632 de Lichtenberg U et al. 2005; PMID: 16278933 Tu BP et al. 2005; PMID: 16254148

and to be clear, I should add that from the data I've looked at, it is plausible that these 3 genes are transcription factors, but I have not seen any evidence showing that any of them actually have this function. Perhaps the Horak et al statement was based on sequence similarity, but I haven't seen any published information to that effect either.

-Karen

Original comment by: krchristie

[gocentral]

For DNA binding, I was more interested in where that came from for TOS4 and PLM2. These have FHA (Forkhead Associated) domains.

Like I said in my last comment, it is plausible that these are transcription factors, but NOT proven in S cerevisiae. If the keywords are based on the Horak paper's untraceable statement, then these transcription keywords should perhaps not be associated with the S. cerevisiae proteins. If the S. pombe Tos4 protein is shown to have that activity, then those keywords can be associated with it, and SGD can ISS to the pombe protein.

-Karen

Original comment by: krchristie

[gocentral]

OK in that case I agree I need to remove my annotations. The trascription role is likely but not unequivocal. I'll wait for Jurg to publish and add transcription related terms back if appropropiate at this point. I don't see any compelling evidence form the sequence as FHA can occur in non-transccription factors. It seems likely that all of the keywords were derived from these older statements

Thanks for the clarification

VAl

Val

Original comment by: ValWood

[gocentral]

Kati has now removed these KWs from TOS4 and PLM2 and updated other relevant annotation in these entries,

With regards to TOS8, there isn't Horak et al paper in the entry or KWs Transcription, Transcription regulation, only DNA-binding KW, and that one is there because the protein contains 1 homeobox DNA-binding domain.

Original comment by: edimmer

[gocentral]

• status: open --> closed

Original comment by: edimmer

[gocentral]

great, that sounds perfect.

thanks,

-Karen

Original comment by: krchristie