TAIR function terms-Nov, 2005

[gocentral]

Hi,

I have 23 function terms from TAIR that I would like to add to GO in the coming week. I am not quite sure about the parentage for some. I would really appreciate if you can give me any feedback on these terms.Thanx

Cheers, Suparna

Here they are:

1. Xanthophyll binding ISA Isoprenoid binding GO:0019840 Def: Interacting selectively with xanthophylls, any of several neutral yellow to orange carotenoid pigments containing oxygen. Ref: ISBN 0-12-214674-3

2. 2-methyl-6-phytyl-1,4-benzoquinone /2-methyl-6- solanyl-1,4-benzoquinone methyltransferase ISA S- adenosylmethionine-dependent methyltransferase activity GO:0008757 Def: catalysis of the reaction: 2-methyl-6-phytyl-1,4- benzoquinone + S-adenosyl-methionine = 2,3-dimethyl-6- phytyl-1,4-benzoquinone + S-adenosyl-homocysteine, or: 2-methyl-6-solanyl-1,4-benzoquinone + S-adenosyl- methionine = 2,3-dimethyl-6-solanyl-1,4-benzoquinone

   • S-adenosyl-homocysteine Ref: PMID:14508009 Exact Synonym: MPBQ/MSBQ METHYLTRANSFERASE

3. red chlorophyll catabolite reductase activity ISA oxidoreductase activity ??? GO:0016491 Def: Catalyzes the ferredoxin dependant reduction of a double bond in the pyrrole system of red chlorophyll catabolite to a colorless tetrapyrrole with a strong blue fluorescence. Ref: ISBN:094308399

4. pentacyclic triterpene synthetase activity ISA intramolecular transferase activity GO:0016866 Def: catalyzes the sythesis of pentacyclic triterpenoids. Ref: PMID:11247608

5. phosphoglucan, water dikinase activity ISA phosphotransferase activity, paired acceptors GO:0016781 Def: Catalysis of the reaction: ATP + glucan-Pn + H2O = AMP + glucan-γPn+1 + phosphate. Ref: PMID: 15618411

6. (Better name) tRNA ligase activity involved in tRNA splicing ISA tRNA ligase activity GO:0004812 Def: three intrinsic activities: an N-terminal adenylyltransferase domain that resembles T4 RNA ligase 1, a central domain that resembles T4 polynucleotide kinase (without 30-phosphatase activity) and a C-terminal cyclic phosphodiesterase (CPDase) domain that is reminiscent of the 2H phosphotransferase enzyme superfamily (13–15). The multifunctional yeast tRNA ligase performs a series of reactions: (i) the 20,30-cyclic phosphate at the end of the 50 tRNA half is hydrolysed by the CPDase activity to generate a 20-phosphate and 30-OH; (ii) the 50-OH group at the end of the 30 tRNA half is phosphorylated by the GTP-dependent kinase activity and (iii) the ligase protein is adenylylated and the AMP is transferred to the 50-phosphate of the 30 tRNA half followed by the formation of the 20- phosphomonoester–30,50-phosphodiester bond and the release of AMP Ref: PMID: 15653639

7. 3,8-divinyl protochlorophyllide a 8-vinyl reductase activity ISA oxidoreductase activity GO:0016491 Def: Catalyzes the conversion of divinyl chlorophyllide to monovinyl chlorophyllide. Ref: PMID: 15632054

8. ammonium (NH3) transporter activity ISA transporter activity GO:0005215 Def: Enables the directed movement of ammonium (NH3 form) into, out of, within or between cells. Ref: PMID:15665250

Note: we also need to modify the definition of the existing ammonium transporter term to avoid defining ammonium exclusively as NH4+, the ref below states ammonium refers to both NH3 and NH4+

9. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity ISA oxidoreductase activity GO:0016491 Def: Catalysis of the reaction: (E)-4-hydroxy-3- methylbut-2-en-1-yl diphosphate + NAD(P)H = isopentenyl diphosphate + NAD(P)+ + H2O. Note that (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate is an alternative way of naming 1-hydroxy-2-methyl-2-(E)- butenyl 4-diphosphate. Ref: PMID: 15863698

10. miRNA methyltransferase activity ISA RNA methyltransferase activity GO:0008173 Def: Catalysis of the transfer of a methyl group to miRNA molecule. Ref: PMID: 15705854

11. sorbitol transporter activity ISA polyol transporter activity GO:0015166 Def: Enables the directed movement of sorbitol into, out of, within or between cells. Sorbitol (D- glucitol) is one of the ten stereoisomeric hexitols. Ref: PMID: 15598803

12. alpha-1, 4-mannosyltransferase activity ISA mannosyltransferase activity GO:0000030 Def: Catalysis of the transfer of a mannose residue from GDP-mannose to an oligosaccharide, forming an alpha-1,4-linkage. Ref: 15772281

13. thalianol synthase activity ISA oxidosqualene cyclase activity GO:0031559 Def: Catalysis of the cyclization of (S)-2, 3- oxidosqualene to thalianol. Ref: PMID 15125655

14. DNA demethylase activity ISA catalytic activity GO:0003824 Def: Catalysis of the reaction involving hydrolytic removal of methyl residues from methyl cytosine in DNA. Ref: PMID: 10085064

15. carboxyltransferase alpha subunit activity ISA ligase activity GO:0016874 Def: Is a component of the acetyl-CoA carboxylase complex. It catalyzes the half reaction: BCCP-CO2- + acetyl-CoA = BCCP + malonyl-CoA Ref: pubmed: 15215578

16. sesquiterpene synthase activity ISA sesquiterpene synthase (new) ISA terpene synthase (new) ISA carbon- carbon lyase (GO:0016830) Def: Catalyzing the formation of sesquiterpenes, from allylic prenyl diphosphate intermediates of the terpene biosynthesis pathway. Ref: TAIR:tb

17. UDP-sugar pyrophosphorylase ISA nucleotidyltransferase activity GO:0016779 Def: Catalysis of the reaction: monosaccharide 1- phosphate + UTP = UDP-sugar + pyrophosphate. Ref: PMID 15326166

Note: all terms acting as uridylyltransferases on monosaccharides 1-phosphate should be children of this new term (see for example GO:0003983, GO:0003982, GO:0017103 or GO:0047338)

18. ethylene binding ISA hormone binding GO:0042562 Def: Interacting selectively with the plant hormone ethylene. Ref: TAIR:sm

19. IAA carboxyl methyltransferase activity ISA carboxyl methyltransferase ISA GO:0008168 Def: Catalysis of the reaction: IAA + S-adenosyl- methionine = MetIAA + S-adenosyl-homocysteine Ref: PMID: 16169896

20. delta 3,5-delta2,4-dienoyl-coA isomerase activity ISA intramolecular oxidoreductase activity, transposing C=C bonds GO:0016863 Def: catalyzes the conversion of 3, 5-dienoyl-CoA to 2,4-dienoyl-CoA Ref: PMID: 16040662

21. siRNA methyltransferase activity ISA RNA methyltransferase activity GO:0008173 Def: Catalysis of the transfer of a methyl group to a siRNA molecule. Ref: TAIR:tb

22. ent-kaurenoic acid oxidase activity ISA oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD or NADH as one donor, and incorporation of one atom of oxygen GO:0016709 Def: Catalysis of three successive oxidations of the C-7 position of the GA skeleton resulting in the conversion of kaurenoic acid to GA12. Ref: PMID: 11172076

23. mannan synthase activity ISA cellulose synthase activity GO: 0016759 Def: Catalyzes the synthesis of B-1,4-mannan backbone of galactomannan, a hemicellulose storage polysaccharide. Ref: PMID: 14726589

Reported by: smundodi

Original Ticket: "geneontology/ontology-requests/3020":https://sourceforge.net/p/geneontology/ontology-requests/3020

[gocentral]

TAIR function terms _nov 2005

Original comment by: smundodi

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Hi Suparna,

Regarding #6, I have a good review on this and will look into it next week.

6. (Better name) tRNA ligase activity involved in tRNA splicing ISA tRNA ligase activity GO:0004812 Def: three intrinsic activities: an N-terminal adenylyltransferase domain that resembles T4 RNA ligase 1, a central domain that resembles T4 polynucleotide kinase (without 30-phosphatase activity) and a C-terminal cyclic phosphodiesterase (CPDase) domain that is reminiscent of the 2H phosphotransferase enzyme superfamily (13–15). The multifunctional yeast tRNA ligase performs a series of reactions: (i) the 20,30-cyclic phosphate at the end of the 50 tRNA half is hydrolysed by the CPDase activity to generate a 20-phosphate and 30-OH; (ii) the 50-OH group at the end of the 30 tRNA half is phosphorylated by the GTP-dependent kinase activity and (iii) the ligase protein is adenylylated and the AMP is transferred to the 50-phosphate of the 30 tRNA half followed by the formation of the 20- phosphomonoester–30,50-phosphodiester bond and the release of AMP Ref: PMID: 15653639

Regarding these two, #10 and #21, I have a question. Is there really anything specific about methyltransferases that act on siRNA or miRNA respectively. Personally, I think it would be good to look into whether these molecular activities are really specific for those types of substrates or are general enzymes that do those types of substrates as well as other types of substrates. If it is the latter situation, then I think these should not be specific function terms, but that methylation of miRNA or siRNA should be represented with process terms instead.

10. miRNA methyltransferase activity ISA RNA methyltransferase activity GO:0008173 Def: Catalysis of the transfer of a methyl group to miRNA molecule. Ref: PMID: 15705854

11. siRNA methyltransferase activity ISA RNA methyltransferase activity GO:0008173 Def: Catalysis of the transfer of a methyl group to a siRNA molecule. Ref: TAIR:tb

-Karen

Original comment by: krchristie

[gocentral]

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my two small units of currency:

> 3. red chlorophyll catabolite reductase activity ISA > oxidoreductase activity ??? GO:0016491 > Def: Catalyzes the ferredoxin dependant reduction of

typo - should be 'ferredoxin-dependent'

> 4. pentacyclic triterpene synthetase activity ISA > intramolecular transferase activity GO:0016866 > Def: catalyzes the sythesis of pentacyclic > triterpenoids.

It would be good to make this def a bit more specific, to make it clear that it represents an activity and shouldn't really be a process.

> 6. (Better name) tRNA ligase activity involved in > tRNA splicing

I agree that this needs a different name - it's not consistent with our function term guidelines to make distinctions, or name terms, in the function ontology based on which process an activity or gene product is involved in. Also, it sounds like the protein you want to annotate has several activities -- but presumably Karen will find out what's going on.

> 8. ammonium (NH3) transporter activity [snip] > Note: we also need to modify the definition of the > existing ammonium transporter term to avoid defining > ammonium exclusively as NH4+, the ref below states > ammonium refers to both NH3 and NH4+

No - the definition is correct. Ammonium is NH4+; NH3 is ammonia. The paper deliberately ignores the distinction for convenience, but GO should use the precise chemical definitions. If the new function term is meant to be specific for NH3, its name and definition should say 'ammonia'

> 15. carboxyltransferase alpha subunit activity ISA > ligase activity GO:0016874 > Def: Is a component of the acetyl-CoA carboxylase > complex. It catalyzes the half reaction: BCCP-CO2- + > acetyl-CoA = BCCP + malonyl-CoA

This is a bad name for a function term; both the name and def should be based on the activity that the term represents, not on anything about complex subunits.

> 19. IAA carboxyl methyltransferase activity

Might be a good idea to spell out indole acetic acid in the term name and def, and use IAA in an exact synonym.

I agree with Karen on #10 and #21. The rest (i.e. anything not mentioned above) look OK to me.

m

Original comment by: mah11

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Hi,

Following discussion with the curators here, who had suggested some of these terms, I would like to drop few terms from the list.

1. pentacyclic triterpene synthetase activity (found the right alternative)

2. carboxyltransferase alpha subunit activity

3. miRNA methyltransferase activity (will add process term instead)

4. siRNA methyltransferase activity (will add process term instead)

'ammonium (NH3) transporter activity' should be 'ammonia(NH3) transporter activity' Will change that term name and definition.

Will wait to hear back from Karen on #6 (tRNA ligase activity)

Thanx for the feedback.

Suparna

Original comment by: smundodi

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Hi Suparna,

For your #6, the term you're talking about "tRNA ligase activity ; GO:0004812" is NOT the enzyme that is involved in splicing the introns that occur in tRNAs (and occasionally in other RNA types). This term refers to the class of activities that charge a tRNA by adding an amino acid to the tRNA. Currently this term has two roots to parent:

molecular_function .catalytic activity ..ligase activity ...ligase activity, forming phosphoric ester bonds ....RNA ligase activity .....tRNA ligase activity ...ligase activity, forming carbon-oxygen bonds ....ligase activity, forming aminoacyl-tRNA and related compounds .....tRNA ligase activity

It might be worth checking whether this type of tRNA ligase should really have parentage under "RNA ligase activity" and thus under "ligase activity, forming phosphoric ester bonds". I kind of wonder if it should really have parentage under both that term AND "ligase activity, forming carbon-oxygen bonds", but the review I'm looking at is only on the splicing of introns from tRNAs, not the charging reaction, so I'll leave that for the moment, and hopefully someone else to check out. It might also be worth investigating if there is another name that could be used for this term that is less ambiguous and the "tRNA ligase" name could be made a synonym.

Going back to the subject of splicing introns from tRNA, the tRNA ligase that performs this in S. cerevisiae is a multifunctional enzyme with three distinct activities: a phosphodiesterase activity, a polynucleotide kinase activity, and RNA ligase activity. It may be worth noting that metazoans seem to have two different redundant mechanisms for religating the two halfs of a cleaved pre- tRNA, one of which is mechanistically the same as that of cerevisiae and one which is not. The mechanism is not yet known in Archaea.

in SGD currently, the TRL1 gene, which encodes the tRNA ligase that is involved in splicing is annotated to only one function term: "RNA ligase (ATP) activity ; GO:0003972". Clearly, it should be annotated to additional function terms. I am not yet sure what terms should be used, or whether appropriate terms already exist. I'll look into that in the next week or so because SGD should really have this enzyme fully annotated.

-Karen

Original comment by: krchristie

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Let me move the #6 from this list to make a new sourceforge entry since the title of this entry 'TAIR function terms' may not interest people who are experts in tRNAs. Hope that can help.

Suparna

Original comment by: smundodi

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Let me move the #6 from this list to make a new sourceforge entry since the title of this entry 'TAIR function terms' may not interest people who are experts in tRNAs. Hope that can help.

Suparna

Original comment by: smundodi

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Sounds like a good idea to move #6 to a new SF item, so that people like Harold will see it and comment.

thanks,

-Karen

Original comment by: krchristie

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Hello Suparna, Just a few (!) comments on your new terms...:

2. 2-methyl-6-phytyl-1,4-benzoquinone /2-methyl-6- solanyl-1,4-benzoquinone methyltransferase --> this should be two separate reactions:

2-methyl-6-phytyl-1,4-benzoquinone methyltransferase activity Catalysis of the reaction: 2-methyl-6-phytyl-1,4-benzoquinone + S- adenosyl-methionine = 2,3-dimethyl-6-phytyl-1,4-benzoquinone + S- adenosyl-homocysteine MetaCyc:RXN-2542 see http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-2542

2-methyl-6-solanyl-1,4-benzoquinone methyltransferase activity 2-methyl-6-solanyl-1,4-benzoquinone + S-adenosyl-methionine = 2,3- dimethyl-6-solanyl-1,4-benzoquinone + S-adenosyl-homocysteine MetaCyc:RXN-2762 see http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-2762

3. red chlorophyll catabolite reductase activity --> can define slightly more accurately: Catalysis of the reaction: red chlorophyll catabolite (RCC) + reduced ferredoxin + 2H+ = primary fluorescent catabolite (pFCC) + oxidised ferredoxin. This reaction is the reduction of the C20/C1 double bond in the pyrrole system of red chlorophyll catabolite to a colorless tetrapyrrole with a strong blue fluorescence. PMID:10743659 EC:1.3.7.- parent: oxidoreductase activity, acting on the CH-CH group of donors, iron- sulfur protein as acceptor ; GO:0016636

4. phosphoglucan, water dikinase activity --> the def has some Greek characters in it, which we usually spell out in GO terms. I couldn't get the full text of the paper - should the reaction should be something like this? Catalysis of the reaction: ATP + glucan-phosphate(n) + H2O = AMP + glucan-gamma-phosphate(n+1) + phosphate.

5. 3,8-divinyl protochlorophyllide a 8-vinyl reductase activity --> is that this reaction? http://biocyc.org/META/NEW-IMAGE? type=REACTION&object=RXN1F-72 Catalysis of the reaction: divinyl protochlorophyllide a + NADPH + H+ = monovinyl protochlorophyllide a + NADP+. MetaCyc:RXN1F-72

6. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity --> think this is EC:1.17.1.2 / MetaCyc:1.17.1.2-RXN http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=1.17.1.2-RXN

7. thalianol synthase activity --> from the abstract, the def should be Catalysis of the cyclization of 3(S)-oxidosqualene to (3S,13S,14R)- malabarica-8,17,21-trien-3-ol (thalianol).

8. DNA demethylase activity --> new def: Catalysis of the reaction: methyl-dCpdG DNA + H2O = dCpdG DNA + methanol. This reaction is the hydrolytic removal of the methyl group on the 5 position of cytosine in DNA. PMID:10050851

9. sesquiterpene synthase activity ISA terpene synthase activity --> have you got a paper reference for these? I think we could get some more accurate names / defs.

10. ent-kaurenoic acid oxidase activity --> This is actually three reactions, so it should be a process, or else we should create a function term for each reaction and put 'ent-kaurenoic acid oxidase' as the synonym. The reactions are: http://biocyc.org/META/NEW-IMAGE?type=REACTION-IN- PATHWAY&object=RXN1F-159 http://biocyc.org/META/NEW-IMAGE?type=REACTION-IN- PATHWAY&object=RXN1F-160 http://biocyc.org/META/NEW-IMAGE?type=REACTION-IN- PATHWAY&object=RXN1F-161

I would suggest it would be better to use a process term such as 'GA12 biosynthesis from ent-kaurenoic acid', with the synonym 'ent-kaurenoic acid oxidase activity'

23. mannan synthase activity --> I think this is analogous to 'glucomannan 4-beta-mannosyltransferase activity ; GO:0047259'. The paper says that the galactomannan has a backbone made of beta-1,4-linked mannosyl residues; if you look at other papers mentioning mannan synthases, they all talk about GDP, so I think the def should be something like:

Catalysis of the reaction: glucomannan(n) + GDP-mannose = glucomannan(n +1) + GDP. PMID: 14726589

Original comment by: girlwithglasses

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Hi Amelia,

Ok, here are the updates for yours:

- #2 is fine to be split into two.

- like the improvised definition of #3

- Here is the definition from the paper for #5 glucan-Pn + ATP + H2O -> Glucan-Pn+1 + AMP + Pi Here is the link to the pdf: http://tesuque.stanford.edu:8080/pub/pdfs/32371.pdf

- #7 and #9 are correct (got an yes from the metacyc curators here, so i guess we are OK here)

- Ok on the definition of #13 and #14

- #16 here is the paper http://tesuque.stanford.edu:8080/pub/pdfs/34292.pdf PMID:15918888 May be we can improvise on the definition but I think the name sounds OK to me. What do you not like about the names? Here is what I found from the paper:

terpene synthase: catalyze the formation of C5, C10, C15 and C20 terpene skeletons from allylic prenyl diphosphate intermediates of the terpene biosynthesis pathway, including dimethylallyl diphosphate (DMAPP,C5), geranyl diphosphate (GPP, C10), farnesyl diphosphate(FPP, C15) and geranylgeranyl diphosphate (GGPP, C20)

Sesquiterpene synthase: catalyzes the formation of (-)-(E)-beta-caryophyllene, alpha-humulene, (-)-alpha-copaene, and beta-elemene.

If you find anything better, please go ahead and add it.

- for #22 here is the response from the metacyc curator: you can keep only one function term for this enzyme. You do not have to create two more. This is a well defined enzyme activity found under EC 1.14.13.79 see: http://www.ebi.ac.uk/intenz/query? cmd=SearchEC&ec=1.14.13.79

the enzyme has three consecutive activities. We cannot just have the process annotation as when we'll run the pub to aracyc pipeline we'll need to retrieve those function annotations. The process annotation would have to be the pathway itself not just a subset of reactions.

- #23 I am not if that is clear from the refenence given here. Can you send me the other references you were talking about mannan synthase is refered as 'glucomannan 4-beta-mannosyltransferase'

I guess the last one is the only outstanding issue now. Once we are in agreement with this, we can proceed with adding these terms to GO.

Sorry it took me longer..

Cheers, Suparna

Original comment by: smundodi

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Update: added the following terms:

1. Xanthophyll binding xanthophyll binding, GO:0051738 (is_a 'pigment binding ; GO:0031409', is_a 'isoprenoid binding ; GO:0019840')

2. 2-methyl-6-phytyl-1,4-benzoquinone /2-methyl-6-solanyl-1,4- benzoquinone methyltransferase 2-methyl-6-phytyl-1,4-benzoquinone methyltransferase activity, GO: 0051741 (is_a 'S-adenosylmethionine-dependent methyltransferase activity ; GO:0008757') 2-methyl-6-solanyl-1,4-benzoquinone methyltransferase activity, GO: 0051742 (is_a 'S-adenosylmethionine-dependent methyltransferase activity ; GO:0008757')

3. red chlorophyll catabolite reductase activity red chlorophyll catabolite reductase activity, GO:0051743 (is_a 'oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor ; GO:0016636')

4. 3,8-divinyl protochlorophyllide a 8-vinyl reductase activity 3,8-divinyl protochlorophyllide a 8-vinyl reductase activity, GO:0051744 (is_a 'oxidoreductase activity ; GO:0016491')

5. ammonium (NH3) transporter activity ammonia transporter activity, GO:0051739 (is_a 'transporter activity ; GO: 0005215')

6. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity, GO: 0051745 (is_a 'oxidoreductase activity, acting on CH2 groups, NAD or NADP as acceptor ; GO:0016726')

7. sorbitol transporter activity was already present - sorbitol == glucitol GO:0015576: name has changed from 'glucitol transporter activity' to 'sorbitol transporter activity'

8. alpha-1,4-mannosyltransferase activity alpha-1,4-mannosyltransferase activity, GO:0051751 (is_a 'mannosyltransferase activity ; GO:0000030')

9. thalianol synthase activity thalianol synthase activity, GO:0051746 (is_a 'oxidosqualene cyclase activity ; GO:0031559')

10. DNA demethylase activity DNA demethylase activity, GO:0051747 (is_a 'hydrolase activity ; GO: 0016787')

11. UDP-sugar pyrophosphorylase UDP-sugar pyrophosphorylase activity, GO:0051748 (is_a 'nucleotidyltransferase activity ; GO:0016779')

12. ethylene binding ethylene binding, GO:0051740 (is_a 'hormone binding ; GO:0042562')

13. IAA carboxyl methyltransferase activity indole acetic acid carboxyl methyltransferase activity, GO:0051749 (is_a 'methyltransferase activity ; GO:0008168')

14. delta 3,5-delta2,4-dienoyl-coA isomerase activity delta3,5-delta2,4-dienoyl-CoA isomerase activity, GO:0051750 (is_a 'intramolecular oxidoreductase activity, transposing C=C bonds ; GO: 0016863')

Original comment by: girlwithglasses

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The remaining terms are:

4. pentacyclic triterpene synthetase activity
5. phosphoglucan, water dikinase activity
6. sesquiterpene synthase activity, terpene synthase activity
7. ent-kaurenoic acid oxidase activity
8. mannan synthase activity

re: 5. phosphoglucan, water dikinase I couldn't access the paper so I have used that def you put in your last reply.

phosphoglucan, water dikinase activity ; GO:0051752

re: 23. mannan synthase activity from PMID:14726589: "Galactomannan is made by the combined actions of two enzymes: mannan synthase (ManS), which makes beta-1,4-linked mannan backbone, and beta- galactosyltransferase, which adds galactosyl residues to the mannan backbone"

"The other polymerizing glycosyltransferase activities that utilize different uridine diphosphate (UDP)-sugar substrates did not appear to be significantly affected in the transgenic soybean somatic embryos expressing the ManS gene in comparison to the control embryos, indicating that the enzyme encoded by the transgene is specific to guanosine diphosphate (GDP)- mannose (fig. S5). Thus, we conclude that the guar ManS gene does indeed encode ManS activity."

The defs for the mannosyltransferase (GO:0000030) terms are either Catalysis of the transfer of a mannose residue from GDP-mannose to an oligosaccharide, forming an alpha/beta-1,x-linkage.

or

Catalysis of the reaction: substrate + GDP-mannose = mannosyl-substrate + GDP.

Mannan is a polymer of beta-1,4-linked mannose residues; the specific reaction that mannan synthase is performing is

mannan + GDP-mannose = mannosyl-mannan (i.e. mannan) + GDP

which is better written as

mannan(n) + GDP-mannose = mannan(n+1) + GDP.

galactomannan is mannan with some galactose residues attached, so the reaction would be

galactomannan(n) + GDP-mannose = galactomannan(n+1) + GDP

which is analogous to the reaction for 'glucomannan 4-beta- mannosyltransferase' that I mentioned before.

Re: 22. ent-kaurenoic acid oxidase activity

A GO function is supposed to be one step in a pathway or one reaction; the enzyme ent-kaurenoic acid oxidase catalyzes three successive reactions, so we should have a function term for each of them. They can all be given the synonym 'ent-kaurenoic acid oxidase', though, to represent the fact that they're all catalyzed by the same reaction. Hey, three annotations for the price of one - that can't be bad! ;)

Re: 4. pentacyclic triterpene synthetase activity

16. sesquiterpene synthase activity, terpene synthase activity

Unfortunately I couldn't access the paper you suggested for the latter terms. :| Generally with these terms, though, I want to be able to make terms for the specific reactions that are occurring, the specific steps of terpene metabolism that these terms are going to represent. I have a feeling that 'xxx synthase' is just being used to represent any enzyme involved the synthesis of xxx, without any specificity regarding what the actual reaction being catalyzed is. If we can narrow down some specific reactions, then I'll add terms for them. :)

Original comment by: girlwithglasses

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-Convinced about the mannan synthase definition. Makes sense now. Thanx

-Regarding ent-kaurenoic acid oxidase activity, I had some more discussion with the metacyc curator here who had proposed this term originally. His argument is, since 'ent' is catalysing all 3 reaction and there is no intermediate release, this should be one reaction. All 3 metacyc references will go to this one enzyme which has 3 reactions in the definiton. This is also important from the curator perspective. A curator who is annotating a gene may not know to use all 3 reactions if they are separated into 3 terms, unless it is clearly mentioned in the definition to use other 2 reactions as well to complete the annotations.

If you don't agree with the above argument, please tell me how GO function terms for multireactions are handled.

- Don't need pentacyclic triterpene.... I have added comment about obsoleting this term below.

Suparna

Original comment by: smundodi

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here is the single reaction for ent.....according to our metacyc curator

Catalysis of three successive oxidations of the C-7 position of the GA skeleton resulting in the conversion of kaurenoic acid to GA12. The total reaction equals to: ent- kaurenoic acid + 3 NADPH + 3 H+ + 3 O2 = GA12 + 3 NAPD+ + 4 H2O.

Suparna

Original comment by: smundodi

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Hi Suparna,

I've added the mannan synthase term:

mannan synthase activity ; GO:0051753

Re: ent-kaurenoic acid oxidase - it would be easy enough to say something in the term defs like:

Catalysis of the reaction: xxx + yyy = aaa + bbb. This is the first/second/ third of three successive oxidations at the C-7 position of the GA skeleton, resulting in the conversion of kaurenoic acid to GA12.

The criteria that we use to decide whether or not a multistep reaction should be a function or not is whether the intermediates are stable and can persist in a cell (e.g. some intermediates might immediately isomerize into a different chemical or react with another substance without any further catalysis). Since GA12 aldehyde is definitely stable and can be used by a different enzyme to synthesize GA14 aldehyde (see http://biocyc.org/META/NEW-IMAGE? type=PATHWAY&object=PWY1F-141&detail-level=2), I think that these reactions do need to be split up.

Original comment by: girlwithglasses

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Also added sesquiterpene metabolism, GO:0051761 (is_a 'terpene metabolism ; GO: 0042214') sesquiterpene biosynthesis, GO:0051762 (is_a 'sesquiterpene metabolism ; GO: 0051761', is_a 'terpene biosynthesis ; GO:0046246') sesquiterpene catabolism, GO:0051763 (is_a 'sesquiterpene metabolism ; GO: 0051761', is_a 'terpene catabolism ; GO:0046247') for process annotation of the sesquiterpene synthases.

Original comment by: girlwithglasses

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OK, you win.. Go ahead and make 3 reactions for the ent- kaurenoic acid oxidase activity. Agree that GA12 aldehyde makes GA14 aldehyde and according to GO norms, I guess we need more than one reaction. What about ent-7-α- hydroxykaurenoate? Is this involved in anything other than this as well? May be in bacteria? I don't know. But please make sure the definition clearly mentions that there are other reactions for this gene product just to make sure the annotators don't end up making mistake by using one of these reactions and not all three. Is it possible to mention the GO ids of other 2 reactions in the definition to be more explicit? Just curious - why can't GO include all the reaction in one term if it is part of a successive reaction? Eventhough the intermediate products are stable and can make something else other than the reaction we are talking about, it is still very much a part of the reaction of converting A -> B right? I am not totally convinced:)

Suparna

Original comment by: smundodi

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OK, I've added those three reactions:

ent-kaurene oxidase activity ; GO:0051777 ent-7-alpha-hydroxykaurene oxidase activity ; GO:0051778 gibberellin 12-aldehyde oxidase activity ; GO:0051779

defs: Catalysis of the reaction: xxx + yyy = aaa + bbb. This is the first/second/third of three successive reactions resulting in the oxidation of ent-kaurenoate (ent-kaurenoic acid) to gibberellin 12 (GA12). comment: Note that the enzyme ent-kaurenoate oxidase also catalyzes the reactions represented by the molecular function terms [term names/IDs of the other two reactions].

> Just curious - why can't GO include all the reaction in one > term if it is part of a successive reaction?

Because of the way that the function ontology was specified - it's supposed to represent single steps at the level of the molecule. We could take a broader view, as you say, and have these three successive reactions represented as a single reaction; similarly we could have photosynthesis represented as a single reaction and not split it up into a series of steps. OTOH, we could take a more detailed approach and look at what's occurring at the submolecular level, and have terms for each bit of the reaction, e.g. substrate binding, nucleophilic attack on xxx, electron donation to yyy, etc., etc.. Trying to decide what level of detail is useful without missing out info or being overinformative is pretty tricky, especially when different papers give different amounts of information on things. The problem is made worse when you're looking at enzymes, because enzymes often catalyze a number of reactions, and the enzyme name doesn't always reflect that. The Enzyme Commission also use a slightly different method of classification to that in GO, so there's not always a 1:1 mapping between the two, and a single enzyme might require several function terms.

I think that 'ent-kaurenoate oxidase activity' would really have been better represented as a process term such as 'ent-kaurenoate oxidation to gibberellin 12' [I thought I suggested that but looking through the comments, I don't know if I did! Doh...], but it's more natural to associate enzymes with function terms.

OK, ramble over... is this item finished now?

Cheers! Amelia.

Original comment by: girlwithglasses

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Happy New year Amelia!

We still need to deal with sesquiterpene synthases.

I think this is the last one on this entry

Suparna

Original comment by: smundodi

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How about we define sesquiterpene synthases as a grouping term which catalyzes FPP to various sesquiterpenes. It is helpful to have a generic term to group these enzymes under one umbrella. In the paper I sent you, authors mention about the gene encoding STS and it catalyzes reaction that results in different STSs. It catalyzes the conversion of FPP into group A sesquiterpenes such as (-)- alpha-copaene, alpha-humulene, and (- )-(E)-beta-caryophyllene and beta-elemene.

So, can we have 2 broad level terms 'terpene synthase' and 'sesquiterpene synthase' and may be 'mono-', 'di-', and 'tri' terpenes. Otherwise we will have to add each one of these reactions which could be hundreds and the gene gets annotated to all those terms. In any case, it will be good to have a broad term that acts as a grouping term for these enzymes.

Suparna

Original comment by: smundodi

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I like Suparna's suggestion of having a broad term. The paper that describes these genes (PMID:15918888) clearly demonstrates that the proteins have the activity of converting FPP to many different sesquiterpenes (all of which have been identified by GS-mass-spec and are listed in Figure 1e of the paper, should you desire to include all their names).

Original comment by: tberardini

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I still don't like Suparna's suggestion, I'm afraid! If you want a general term, you should use the process term 'sesquiterpene biosynthesis', as that represents the formation of any sesquiterpene. I will add 'sesquiterpene synthase activity' as a synonym for searching purposes. For the function ontology, we want specific reactions, not a general term which could represent any of a number of different reactions. Enzyme grouping terms are supposed to group by analogous reactions, not by those reactions that have the same substrate.

The other point is that 'sesquiterpene synthase' is a name that these scientists have given a protein. It's not an accurate description of the reactions this protein is catalyzing. What happens if we add this term, and then another sesquiterpene synthase is found - perhaps in a different species

• which forms a different set of products? The only information we would capture is that both proteins are called sesquiterpene synthases, and all that tells us is that they synthesise sesquiterpenes - i.e. sesquiterpene biosynthesis.

I think this kind of situation will be made less problematic when we start introducing links between process and function, so then there's less of a divide between the two ontologies.

I've added synonyms to the terpene/sesquiterpene biosyn terms, so unless there is anything else outstanding in this item, I think it can be closed.

Cheers! Amelia.

Original comment by: girlwithglasses

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• milestone: --> TermGenie
• assigned_to: smundodi --> girlwithglasses
• status: open --> closed-accepted

Original comment by: girlwithglasses

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What, then, would you suggest using as a function term for annotating these gene products?

Original comment by: tberardini

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Page 10 and 11 have some description and a nice set of diagrams of the reactions. It would probably be good to ask someone in the know about enzyme classification, but it looks like there is a reaction of class 4.2.3 (carbon-oxygen lyase activity, acting on phosphates ; GO:0016838), followed by different isomerizations (isomerase activity ; GO:0016853) and cyclizations (cyclase activity ; GO:0009975).

See http://www.chem.qmul.ac.uk/iubmb/enzyme/EC4/intro.html http://www.chem.qmul.ac.uk/iubmb/enzyme/EC5/intro.html for descriptions of different types of reaction.

Original comment by: girlwithglasses