conserved unknowns changes since publication, reducing log

ValWood commented 6 years ago

CONSERVED UNKNOWN CHANGES 410

Although these were in "conserved unknown" they had an existing process annotation and so they were not in the Open Biology unknown list:

[x] SPBC9B6.03 endosomal transport; GOid=GO:0016197; evidence=ISS; db_xref=GO_REF:0000024; with=UniProtKB:Q7Z3T8;
[x] hdd1 SPCC4G3.17 term=deoxyribonucleoside monophosphate catabolic process; GOid=GO:0009159; evidence=ISO; with=SGD:S000003069
[x] puf2 GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ISO SGD:S000006246
[x] SPBC31F10.10c ubiquitin-dependent protein catabolic process; GOid=GO:0006511; evidence=ISS; with=SGD:S000004706

removed from the open biology unknowns list since publcation, new gene characterizations

gene	ID	GO process	source or comment	date
atg38	--	--	was an orphan, characterized in pombe and other species (broad eukaryotic)
ptf1	--	--	characterized in pombe (broad eukaryotic)
les1	--	--	characterized in pombe (fungal specific)
cue2	--	--	ISS to SGD
rdl2	--	sulfide oxidation, using sulfide:quinone oxidoreductase	from human TSTD1 Q8NFU3 via Reactome
psg1	SPBC21C3.17c	endoplasmic reticulum to Golgi vesicle-mediated transport	ISS to SGD (fungal specific)
psg2	SPCP31B10.04	endoplasmic reticulum to Golgi vesicle-mediated transport	ISS to SGD (fungal specific)
n/a	SPAC2E12.03c	transporter	ISS from human, not sure I belive this, it does not look like a transporter
wdr44	SPAC3H5.08c	exocytosis	NAS PMID:32344433 will update evidence once annotated	20200927

CURRENT TOTAL 406 (becasue some added back)

removed from the open biology unknowns list since publication, should not have been included

gene	ID	GO process	source or comment	date
--	SPCC777.04	transporter
--	SPAC750.08c	-	partial protein
--	SPAC186.04c	-	partial protein
tgs1	SPAC2G11.15c	-	has a process but not in a slim category
bsp1	SPAC9E9.05	-	has a process but not in a slim category
afg1	SPBC115.02c	protein quality control in the mitochondria	was not annotated as unknown, but process was missing	20200930
mac1	SPAC13G7.04c	exocytosis	ISS to mug33, also supported by location and PMID: 33002606

Added into conserved unknowns since publication, existing annotation removed

gene	ID	comment
tfb6	SPCC1494.09c	removed annotation related to transcription TFIIH
Spp41	SPBC17D1.01	removed? (see below)
n/a	SPAC1782.02c	previously had 'mitochondrial genome maintence' by ISS, this is just a phenotype, now unknown

Added to conserved unknowns list (back from published or inferred) CRITERIA STRICTER, or they have a process annotation which resulted in them slimming despite being 'unknown'

gene	ID	comment
dhm1	SPCP1E11.10	it is possible this was previously annotated
cue3	SPCC1906.02c	reverted to unknown, not enough info, but possibly DNA repair
mac1	SPAC13G7.04c	was classed as 'published' but has no process inormation
mug8	SPAC32A11.01	it is possible this was previously annotated
big1	SPCC306.06c	Cell wall biogenesis ISS form SGD was removed as likely indirect effect
cdb4	SPAC23H4.09	was previously classed as published, but changed to unknown, not enough data
ftp105	SPAC17A5.16	it is possible this was previously annotated
mug30		slimmed to protein modification by small protein conjugation or removal in OB paper
n/a	SPBC19G7.04	it is possible this was previously annotated
n/a	SPAP27G11.12	it is possible this was previously annotated
n/a	SPBP19A11.07c	it is possible this was previously annotated
miy1	SPAC12G12.11c	it is possible this was previously annotated
n/a	SPCC4G3.12c	slimmed to protein modification by small protein conjugation or removal in OB paper
meu34	SPAC3A12.03c	slimmed to protein modification by small protein conjugation or removal in OB paper
n/a	SPBC15C4.06c	slimmed to protein modification by small protein conjugation or removal in OB paper
n/a	SPAC6B12.07c	slimmed to protein modification by small protein conjugation or removal in OB paper
n/a	SPAC57A7.09	slimmed to protein modification by small protein conjugation or removal in OB paper
n/a	SPBC14F5.10c	slimmed to protein modification by small protein conjugation or removal in OB paper
n/a	SPBC14F5.10c	slimmed to protein modification by small protein conjugation or removal in OB paper	slimmed to protein modification by small protein conjugation or removal in OB paper
n/a	SPBC25D12.06	too little info to infer process
n/a	SPBC18E5.10	this is one of those weirdo complex I subunits
n/a	SPAC11E3.12	this is one of those weirdo complex I subunits
n/a	SPBC6B1.03c	it is possible this was previously annotated
n/a	SPAC19B12.01	removed cell wall annotation, not enough data, likely indirect
n/a	SPAP8A3.13c	Vid24 family This one is tricky
n/a	SPAC110.01	slimmed to signalling l in OB paper
n/a	SPCC162.10	slimmed to signalling l in OB paper
n/a	SPAC22G7.08	slimmed to signalling l in OB paper
n/a	SPAC23H4.02	slimmed to signalling l in OB paper
n/a	SPAC1F7.06	possibly detoxification but not enough info
n/a	SPCC553.04	not vecessariy protein folding, don't know physiologcial role
ibp1	SPBC839.07	is published but Unknown BP
tpp2	-	is published but Unknown BP
txc1	-	is published but Unknown BP

SPECIES SPECIFIC UNKNOWNS CHARACTERIZED

gene	ID	GO process	source or comment
ebp1	--	--	characterized in pombe (pombe specific)
mtl2	--	--	characterized in pombe PMID:23907979 needs curating (pombe specific)
mtl3	--	--	characterized in pombe PMID:23907979 needs curating (pombe specific)

Misc oddity SPBPJ4664.02 (crazy cell surface protein) has adhesion but is still unknown really

these should be excluded SPBC1711.02	mat3-Mc	mating type M-specific HMG-box DNA-binding transcription factor Mc at silenced MAT3 locus
SPBC1711.01c	mat3-Mi	mating type M-specific polypeptide Mi at silenced MAT3 locus

ValWood commented 6 years ago

Mailed SGD as PMID:28727280 still isn't annotated

[x] SPBC21C3.17c is a Golgi trafficking protein https://www.ncbi.nlm.nih.gov/pubmed/28727280?dopt=Abstract
[x] SPCP31B10.04 paralog

https://github.com/pombase/curation/issues/2637

ValWood commented 6 years ago

[X] SPCC1494.09c tfb6 re- included in unknowns After conversation with Rob Nash at SGD, I am going to revert TFB6 to "unknown" process (and probably remove TFIIIB)

An excerpt:

This 2016 paper does not show it as a bona fida complex member. https://www.ncbi.nlm.nih.gov/pubmed/27381459 Other oddity is that the abstract reports a high similarity to a human protein, but this does not exist. This seems to be fungal specific (which is very rare for general TFs).

I will revert the PomBase annotation to "unknown" process

On 22/08/2018 09:47, Valerie Wood wrote:

Actually, I see what you mean. Although TFB6 is a component of the complex, it may not function in the context of transcription if it is ssl2 for use in other contexts.

only releasing On 22/08/2018 09:38, Valerie Wood wrote:

Hmm, not sure. I'm going to ask for advice on how others would annotate this. To me, it seems odd to say something is core TFIID, and then not have a transcription process based on this observation. But as you say the exact role in transcription is not established (I definitely wouldn't make a "NOT" annotation to show a lack of involvement based on the in vitro assay, because this does not rule out a role in transcription.....

On 17/08/2018 18:55, Rob Nash wrote:

Hi Val,

Thanks for clarifying and providing a possible paper to use in annotation. This subunit was identified much later than the rest of those for TFIID, and the gene/protein has not been well studied. I took a look at the paper you suggested, and in this paper they show no impact on in vitro transcriptional initiation or preinitiation complex (PIC) assembly. Add back experiments did not impact transcriptional initiation either. So I think this why we did not annotate the suggested process, and I am uncomfortable adding an IC followed by a NOT annotation.

The only observation of note in this paper is that in the presence of phosphorylated Tfb6p, the Ssl2p helicase subunit, tends to dissociate from TFIID and forms a heterodimer with Tfb6p. However, if Ssl2p is already assembled into a complete preinitation complex than Tfb6p appears unable to dissociate the helicase. So the only term I have been able come up would be this one:

GO:0034367 protein-containing complex remodeling The acquisition, loss, or modification of macromolecules within a complex, resulting in the alteration of an existing complex.

and the evidence is not strong. In the paper they basically study TFIID subunit composition in the absence and presence of TFB6, and then follow this up by add back experiments where some Ssl2p is now lost from TFIID and appears in complex with Tfb6p.

So I wonder if you have any thoughts on whether this would be an accurate annotation based on the evidence and of use to you. I am on the fence about adding this one.

ValWood commented 6 years ago

[x] Spp41 can only have "regulation of gene expression'

Edith: "Yes, from that paper, I would agree that it is just suppression of a cold phenotype. I've removed that annotation and replaced it with GO:0010629 (Neg. regulation of gene expression, has_input PRP4|PRP3) since there's increase in PRP4 and PRP3 expression in a spp41 mutant."

So, this one will not be specific enough for our slim (could be txn, translation, processing, maturation). This one will come back into "unknowns"

ValWood commented 6 years ago

rdl2,rbd4,rbd3,SPCC777.03 SPAC11D3.10 SPAC23A1.14 seem to be doing something together at the MOM (sulphur metabolism, folding? import? tRNA metabolism)

[x] rdl2 from human TSTD1 Q8NFU3 thiosulfate-thiol sulfurtransferase activity sulfide oxidation, using sulfide:quinone oxidoreductase vai Reactome

Done rdl2, could not track down the connection of annotation for the others

ValWood commented 5 years ago

[x] ess1 name added, but I think this will probably stay as colour10. It's still unknown physiological role. name description, DUF Eight-Six-Six;

authors speculate oxidative phosphorylation, but really its more closely aligned with MAPK pathway and response to oxidative stress.

mah11 commented 5 years ago

I've just done the community session for the ess1 paper

That's great. It's still unknown as I expected since its phenotypes not GO.

yup, and just H2O2 sensitivity at that.

ValWood commented 5 years ago

done everything except SPBC21C3.17c waiting for response from SGD

ValWood commented 5 years ago

SPBC21C3.17 can be annotated,

SGD annotated YKL077W to 'protein maturation'

ValWood commented 4 years ago

Add back to unknowns. Transcription evidence very poor

[x] SPCC553.04WD repeat protein involved in transcriptional regulation (predicted)
[x] cyp9 WD repeat containing cyclophilin family peptidyl-prolyl cis-trans isomerase Cyp9 (predicted)

ValWood commented 4 years ago

obr1 / SPAC3C7.14c details back in unknown Poorly characterized

ValWood commented 3 years ago

still to sort, conserved unknowns absent from OB list

SPBC25D12.06		mitochondrial ATP-dependent RNA helicase (predicted)
SPAC3A12.02		mitochondrial inorganic diphosphatase (predicted)
SPAC12B10.14c	tea5	pseudokinase Tea5
SPAC23A1.14c		pyridoxal phosphate-dependent transferase, unknown specificity, implicated in sulfur compound metabolis

still to sort in OB unknowns list but not in PomBase unknown (conserved or species specific)

SPBC20F10.10	psl1	cyclin pho85 family Psl1 (predicted)
SPBP4G3.02	pho1	extracellular acid phosphatase Pho1
SPAC57A10.04	mug10	meiotic Rho guanine nucleotide exchange factor (predicted)

ValWood commented 3 years ago

[x] mde7 annotate to RNA processing?
[x] SPBC27B12.05 | | WD repeat protein
[x] SPCC1494.09c is now TFIIH complex subunit Tfb6 not sure why this was not annotated
[x] SPAC22F3.04 mug62 acetyl CoA biosynthesis
[x] SPAC56F8.02. acetyl CoA biosynthesis
[x] SPAC17A2.02c plasma membrane organization
[x] SPBC4B4.11 mitochondrial ribosomal protein S41 (conserved unknown)
[x] SPAC20G4.05c -> Protein adenylyltransferase SelO, mitochondrial
[x] SPCC338.04 mitochondrial matrix import factor Mix23
[x] SPBC20F10.02c Golgi to plasma membrane transport protein
[x] SPAP14E8.05c TMEM14C -> mitochondrial transmembrane transport (protoporphyrinogen IX)

ValWood commented 3 years ago

Added back

[x] SPBC26H8.13c add back to unknowns (was apoptotic process)
[x] ecm14, added back, poorly characterised pseudopeptidase
[x] ber1 / SPBC14C8.13 poorly characterized, conflicting annotations

ValWood commented 3 years ago

Back in unknown.
SPBC17D11.08 dca7 WD repeat protein, DDB1 and CUL4-associated factor Dca7 (predicted)

ValWood commented 3 years ago

added back, poorly characterised SPAC1B3.08

ValWood commented 3 years ago

@bahler SPAC18B11.08c will come out of the conserved unknown list this week. It is PAT complex subunit Asterix (it is https://www.pombase.org/gene/SPBC2G5.01 CCCDC47 binding partner) PMID:32814900 PMID:33082068