chaperone activity tree reorg

[gocentral]

Prompted by an earlier source forge item on chaperone activity, I have submitted a proposal for reorganizing the tree. Please give me feed back.

Chaperone tree

Function ontology Proposal ----%chaperone activity(new term) -----------%nucleotide hydrolysis dependent chaperone activity
-----------------%chaperone _cofactor activity dependent chaperone activity (new) -----------------%chaperone_cofactor activity independent chaperone activity(new) ----------%nucleotide hydrolysis independent chaperone activity (new) -----------------%holding chaperone activity (new) -----------------%protein disulfide isomerase (term exists) -----------------%peptidylprolyl isomerase (term exists) ----%binding -----------%protein binding
-----------------% co-chaperone activity (synonyms: chaperone cofactor activity, chaperone activator activity, chaperone regulator activity) (new)

Definitions: Chaperone activity: (NEW) Refers to the activity of assisting in covalent and non-covalent rearrangements in order to fold a macromolecule (such as a polypeptide or nucleic acid) to its correct 3-dimensional structure or properly assemble multi-polypeptide complexes, including those that contain nucleic acids and carbohydrates. This activity is independent of and not part of the activity and function of the final assembled structure or complex.

Nucleotide hydrolysis dependent chaperone activity (new) Refers to the activity of a class of chaperone molecules that assists in the correct non-covalent folding of macromolecules over cycles of nucleotide hydrolysis dependent binding and release. Comment: Consider additional terms ATPase activity and GTPase activity terms.

chaperone_cofactor activity depedent chaperone activity (new) Refers to the activity of a class of chaperone molecules that assist in the correct non-covalent assembly of post-translational proteins and are dependent on additional protein cofactors. This function happens over one or several cycles of nucleotide hydrolysis dependent binding and release.

chaperone_cofactor activity independent chaperone activity (new) Refers to the activity of a class of chaperone molecules that assist in the correct non-covalent assembly of post-translational proteins and do not dependent on additional protein cofactors. This function happens over one or several cycles of nucleotide-dependent binding and release.

Nucleotide hydrolysis independent chaperone activity (new) Refers to the activity of a class of chaperone molecules that assists in the correct folding of macromolecules in the absence of nucleotide hydrolysis.

Holding chaperone activity (new) Refers to the activity of a class of chaperone molecules that hold or sequester macromolecules to prevent their aggregation or misfolding and is independent of nucleotide hydrolysis. Such substrate macromolecules attain their native conformation with the assistance of other chaperone molecules.

Co_chaperone activity Refers to the activity of proteins that activate the chaperone molecule (ring shaped multisubunit complexes) to sequester the misfolded substrates and release the folded products.

The following terms have to be obsoleted.

1) Hsp 70-90 organizing protein (synonym of holding chaperone activity)- mentions specific gene product in the term and this protein (HOP) transfers substrates from Hsp70 to hsp 90.

2) co-chaperone activity (synonym of chaperone cofactor activity) co-chaperonin activity (obsolete) co-chaperones are proteins that bind to chaperones and the complex folds the misfolded proteins. Co-chaperones by themselves do not have chaperone activity. So gene products like GroES, also called co-chaperonin, should be annotated to chaperone cofactor activity. Some of them are nucleotide exchange factors also. Co-chaperones and co-chaperonins are used interchangeably.

3) chaperonin ATPase activity (synonym) consider ATPase activity and the nucleotide hydrolysis dependent chaperone activity terms.

4) glyco-protein specific chaperone activity (obsolete)- consider GO-process term N-linked glycoprotein maturation and nucleotide hydrolysis independent chaperone activity

5) tubulin-specific chaperone activity (obsolete) consider protein complex assembly/tubulin folding and one of the chaperone activity terms

6) fimbrium specific chaperone activity (obsolete) refers to proteins that assist in the linear organization of the protein pilus which forms the tubular structure or the organelle, fimbria (aka pilus) which helps bacteria attach to surface. These proteins are not involved in correcting the folding of pilus, they just help them come together. Consider : protein binding, bridging (GO-function) and fimbrium biogenesis process term. 7) chaperone inhibitor activity (obsolete)- Consider ATPase inhibitor activity, regulation of protein folding (proposing new term in process ontology) and its children terms 8) ribosomal chaperone activity- consider ribosome biogenesis and nucleotide dependent chaperone activity 9) heat shock protein activity: synonym of nucleotide dependent chaperone activity 10) histone chaperone activity (obsolete): Consider histone binding, chromatin assembly/disassembly, nucleosome assembly

In the following terms chaperone has been used to mean carrier/transport These terms have to be children/synonym of some transport term. 1) Copper chaperone activity synonym of copper ion tansporter activity, remove from chaperone activity node 2) Metallo chaperone activity synonym of metal ion transporter activity, remove from chaperone activity node 3) Superoxide dismutase copper chaperone activity (gene product ?obsolete?)- child of copper ion transporter activity, remove from chaperone activity node.

Reported by: rbalakri

Original Ticket: "geneontology/ontology-requests/1427":https://sourceforge.net/p/geneontology/ontology-requests/1427

[gocentral]

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Hi Rama -

These terms names sound a bit odd:

chaperone_cofactor activity depedent chaperone activity chaperone_cofactor activity independent chaperone activity

is there a reason for the underscores? I'd take them out, we don't use them in any other terms names. I'd also take out the first 'activity' from these term names, makes them too confusing.

And would it be possible to remove the references to the activities of classes of proteins from the definitions? e.g.

Nucleotide hydrolysis independent chaperone activity (new) Refers to the activity of a class of chaperone molecules that assists in the correct folding of macromolecules in the absence of nucleotide hydrolysis.

->

Nucleotide hydrolysis independent chaperone activity (new) Catalysis of the correct folding of macromolecules in the absence of nucleotide hydrolysis.

?

Original comment by: jl242

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Hi Rama,

I am not convinced that 'chaperone activity' is really a GO function. The job that these molecules are doing helping out in protein assembly, which is protein binding of some sort or holding things into position. 'Chaperone' is too ambiguous a word to use because it has connotations of accompanying someone/ something (as seen in terms such as metallochaperone). I really think what we have is a process, and that the terms like "chaperone cofactor-dependent chaperone activity" would be better in process somewhere under "protein folding".

Original comment by: girlwithglasses

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Amelia,

I agree to a certain extent that chaperone activity is not a function but more of a process term. There are already few terms in the ontology that use the word chaperone in mean escorting (transporting/accompany) somebody. But Biologists don't use the word chaperone in that context. It is a grey area. I will look into moving some of these into the process ontology. If you have some thoughts, please let me know. Again, I am sorry for prolonging this.

Rama

Original comment by: rbalakri

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Amelia,

I have reworked the tree. I could fit in a lot of terms in the process ontology. Please let me know if I overlooked something.

Thanks,

Rama

Function Ontology- Protein binding %holding chaperone activity (new)

Process ontology Proposal ---------%protein folding -----------------% de novo protein folding (exists) (synonym-nascent chain protein folding) ------------------------% Co-translational/multi domain protein assembly(new)

----------------%post translational protein folding (new) ----------------------------%protein complex assembly(term exists) ------------------------------------%tubulin folding (term exists, move it here) ------------------------------------%cytochrome C biogenesis (term exists, move it here) ------------------------------------%steroid hormone receptor complex assembly (term
exists, move it here) ----------------------------%chaperone _cofactor activity dependent protein folding(new) ---------------------------%chaperone_cofactor activity independent protein folding(new) -----------------%protein refolding (exists) (synonym-Stress response protein folding, heat shock response protein folding)

Definitions: Holding chaperone activity (new)-Function ontology Refers to the activity of a class of chaperone molecules that hold or sequester macromolecules to prevent their aggregation or misfolding and is independent of nucleotide hydrolysis. Such substrate macromolecules attain their native conformation with the assistance of other chaperone molecules

Process Ontology terms Protein folding (exists without definition) Process that assists in the correct non-covalent assembly of single chain polypeptides or multisubunit complexes into its tertiary structure.

Co-translational/multi domain protein assembly (new) Process that assists in the correct non-covalent assembly of the ribosome-bound nascent chains of a multidomain protein, while other parts of the protein are still being translated.

Post translational protein folding (new) Process that assists in the correct non-covalent folding of newly formed polypeptides or folding intermediates of polypeptides that have exited the ribosome and/or have been stabilized and transferred by other chaperone proteins. This process could involve several cycles of ATP hydrolysis.

chaperone_cofactor activity depedent protein folding(new) Process that assists in the correct non-covalent assembly of post-translational proteins and are dependent on additional protein cofactors. This function happens over one or several cycles of nucleotide hydrolysis dependent binding and release.

chaperone_cofactor activity independent protein folding(new) Process that assists in the correct non-covalent assembly of post-translational proteins and do not depend on additional protein cofactors. This function happens over one or several cycles of nucleotide-dependent binding and release.

.

The following terms have to be obsoleted. 1) Chaperone activity- Turns out that ATP hydrolysis dependent chaperone activity is more of a process than one function involving substrate binding and ATP hydrolysis. For those chaperones molecules that just hold an unfolded substrate and prevent them from aggregating, there is a term called holding chaperone activity as a child of protein binding. For GroEL like complexes, you will annotate the subunits to protein binding and/or ATP binding/ATP hydrolysis activity

) Hsp 70-90 organizing protein (synonym of holding chaperone activity)- mentions specific gene product in the term and this protein (HOP) transfers substrates from Hsp70 to hsp 90.

2) co-chaperone activity (synonym of chaperone cofactor activity) co-chaperonin activity (obsolete) co-chaperones are proteins that bind to chaperones and the complex folds the misfolded proteins. Co-chaperones by themselves do not have chaperone activity. So gene products like GroES, also called co-chaperonin, should be annotated to chaperone cofactor activity. Some of them are nucleotide exchange factors also. Co-chaperones and co-chaperonins are used interchangeably. Consider protein binding and the process terms- chaperone_cofactor activity depedent protein folding

3) chaperonin ATPase activity (synonym) consider ATPase activity and the one of the protein folding process terms

4) glyco-protein specific chaperone activity (obsolete)- consider GO-process term N-linked glycoprotein maturation

5) tubulin-specific chaperone activity (obsolete) consider protein complex assembly/tubulin folding

6) fimbrium specific chaperone activity (obsolete) refers to proteins that assist in the linear organization of the protein pilus which forms the tubular structure or the organelle, fimbria (aka pilus) which helps bacteria attach to surface. These proteins are not involved in correcting the folding of pilus, they just help them come together. Consider : protein binding, bridging (GO-function) and fimbrium biogenesis process term. 7) chaperone inhibitor activity (obsolete)- Consider ATPase inhibitor activity, regulation of protein folding (proposing new term in process ontology) and its children terms 8) ribosomal chaperone activity- consider ribosome biogenesis 9) heat shock protein activity (obsolete), consider protein refolding process term 10) histone chaperone activity (obsolete): Consider histone binding, chromatin assembly/disassembly, nucleosome assembly 11)protein assembly, multchaperone pathway (obsolete)-consider one of the other protein assembly process terms.

In the following terms chaperone has been used to mean carrier/transport These terms have to be children/synonym of some transport term. 1) Copper chaperone activity synonym of copper ion tansporter activity, remove from chaperone activity node 2) Metallo chaperone activity synonym of metal ion transporter activity, remove from chaperone activity node 3) Superoxide dismutase copper chaperone activity (gene product ?obsolete?)- child of copper ion transporter activity, remove from chaperone activity node.

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=554736

Amelia,

I have reworked the tree. I could fit in a lot of terms in the process ontology. Please let me know if I overlooked something.

Thanks,

Rama

Function Ontology- Protein binding %holding chaperone activity (new)

Process ontology Proposal ---------%protein folding -----------------% de novo protein folding (exists) (synonym-nascent chain protein folding) ------------------------% Co-translational/multi domain protein assembly(new)

----------------%post translational protein folding (new) ----------------------------%protein complex assembly(term exists) ------------------------------------%tubulin folding (term exists, move it here) ------------------------------------%cytochrome C biogenesis (term exists, move it here) ------------------------------------%steroid hormone receptor complex assembly (term
exists, move it here) ----------------------------%chaperone _cofactor activity dependent protein folding(new) ---------------------------%chaperone_cofactor activity independent protein folding(new) -----------------%protein refolding (exists) (synonym-Stress response protein folding, heat shock response protein folding)

Definitions: Holding chaperone activity (new)-Function ontology Refers to the activity of a class of chaperone molecules that hold or sequester macromolecules to prevent their aggregation or misfolding and is independent of nucleotide hydrolysis. Such substrate macromolecules attain their native conformation with the assistance of other chaperone molecules

Process Ontology terms Protein folding (exists without definition) Process that assists in the correct non-covalent assembly of single chain polypeptides or multisubunit complexes into its tertiary structure.

Co-translational/multi domain protein assembly (new) Process that assists in the correct non-covalent assembly of the ribosome-bound nascent chains of a multidomain protein, while other parts of the protein are still being translated.

Post translational protein folding (new) Process that assists in the correct non-covalent folding of newly formed polypeptides or folding intermediates of polypeptides that have exited the ribosome and/or have been stabilized and transferred by other chaperone proteins. This process could involve several cycles of ATP hydrolysis.

chaperone_cofactor activity depedent protein folding(new) Process that assists in the correct non-covalent assembly of post-translational proteins and are dependent on additional protein cofactors. This function happens over one or several cycles of nucleotide hydrolysis dependent binding and release.

chaperone_cofactor activity independent protein folding(new) Process that assists in the correct non-covalent assembly of post-translational proteins and do not depend on additional protein cofactors. This function happens over one or several cycles of nucleotide-dependent binding and release.

.

The following terms have to be obsoleted. 1) Chaperone activity- Turns out that ATP hydrolysis dependent chaperone activity is more of a process than one function involving substrate binding and ATP hydrolysis. For those chaperones molecules that just hold an unfolded substrate and prevent them from aggregating, there is a term called holding chaperone activity as a child of protein binding. For GroEL like complexes, you will annotate the subunits to protein binding and/or ATP binding/ATP hydrolysis activity

) Hsp 70-90 organizing protein (synonym of holding chaperone activity)- mentions specific gene product in the term and this protein (HOP) transfers substrates from Hsp70 to hsp 90.

2) co-chaperone activity (synonym of chaperone cofactor activity) co-chaperonin activity (obsolete) co-chaperones are proteins that bind to chaperones and the complex folds the misfolded proteins. Co-chaperones by themselves do not have chaperone activity. So gene products like GroES, also called co-chaperonin, should be annotated to chaperone cofactor activity. Some of them are nucleotide exchange factors also. Co-chaperones and co-chaperonins are used interchangeably. Consider protein binding and the process terms- chaperone_cofactor activity depedent protein folding

3) chaperonin ATPase activity (synonym) consider ATPase activity and the one of the protein folding process terms

4) glyco-protein specific chaperone activity (obsolete)- consider GO-process term N-linked glycoprotein maturation

5) tubulin-specific chaperone activity (obsolete) consider protein complex assembly/tubulin folding

6) fimbrium specific chaperone activity (obsolete) refers to proteins that assist in the linear organization of the protein pilus which forms the tubular structure or the organelle, fimbria (aka pilus) which helps bacteria attach to surface. These proteins are not involved in correcting the folding of pilus, they just help them come together. Consider : protein binding, bridging (GO-function) and fimbrium biogenesis process term. 7) chaperone inhibitor activity (obsolete)- Consider ATPase inhibitor activity, regulation of protein folding (proposing new term in process ontology) and its children terms 8) ribosomal chaperone activity- consider ribosome biogenesis 9) heat shock protein activity (obsolete), consider protein refolding process term 10) histone chaperone activity (obsolete): Consider histone binding, chromatin assembly/disassembly, nucleosome assembly 11)protein assembly, multchaperone pathway (obsolete)-consider one of the other protein assembly process terms.

In the following terms chaperone has been used to mean carrier/transport These terms have to be children/synonym of some transport term. 1) Copper chaperone activity synonym of copper ion tansporter activity, remove from chaperone activity node 2) Metallo chaperone activity synonym of metal ion transporter activity, remove from chaperone activity node 3) Superoxide dismutase copper chaperone activity (gene product ?obsolete?)- child of copper ion transporter activity, remove from chaperone activity node.

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=554736

Amelia,

I have reworked the tree. I could fit in a lot of terms in the process ontology. Please let me know if I overlooked something.

Thanks,

Rama

Function Ontology- Protein binding %holding chaperone activity (new)

Process ontology Proposal ---------%protein folding -----------------% de novo protein folding (exists) (synonym-nascent chain protein folding) ------------------------% Co-translational/multi domain protein assembly(new)

----------------%post translational protein folding (new) ----------------------------%protein complex assembly(term exists) ------------------------------------%tubulin folding (term exists, move it here) ------------------------------------%cytochrome C biogenesis (term exists, move it here) ------------------------------------%steroid hormone receptor complex assembly (term
exists, move it here) ----------------------------%chaperone _cofactor activity dependent protein folding(new) ---------------------------%chaperone_cofactor activity independent protein folding(new) -----------------%protein refolding (exists) (synonym-Stress response protein folding, heat shock response protein folding)

Definitions: Holding chaperone activity (new)-Function ontology Refers to the activity of a class of chaperone molecules that hold or sequester macromolecules to prevent their aggregation or misfolding and is independent of nucleotide hydrolysis. Such substrate macromolecules attain their native conformation with the assistance of other chaperone molecules

Process Ontology terms Protein folding (exists without definition) Process that assists in the correct non-covalent assembly of single chain polypeptides or multisubunit complexes into its tertiary structure.

Co-translational/multi domain protein assembly (new) Process that assists in the correct non-covalent assembly of the ribosome-bound nascent chains of a multidomain protein, while other parts of the protein are still being translated.

Post translational protein folding (new) Process that assists in the correct non-covalent folding of newly formed polypeptides or folding intermediates of polypeptides that have exited the ribosome and/or have been stabilized and transferred by other chaperone proteins. This process could involve several cycles of ATP hydrolysis.

chaperone_cofactor activity depedent protein folding(new) Process that assists in the correct non-covalent assembly of post-translational proteins and are dependent on additional protein cofactors. This function happens over one or several cycles of nucleotide hydrolysis dependent binding and release.

chaperone_cofactor activity independent protein folding(new) Process that assists in the correct non-covalent assembly of post-translational proteins and do not depend on additional protein cofactors. This function happens over one or several cycles of nucleotide-dependent binding and release.

.

The following terms have to be obsoleted. 1) Chaperone activity- Turns out that ATP hydrolysis dependent chaperone activity is more of a process than one function involving substrate binding and ATP hydrolysis. For those chaperones molecules that just hold an unfolded substrate and prevent them from aggregating, there is a term called holding chaperone activity as a child of protein binding. For GroEL like complexes, you will annotate the subunits to protein binding and/or ATP binding/ATP hydrolysis activity

) Hsp 70-90 organizing protein (synonym of holding chaperone activity)- mentions specific gene product in the term and this protein (HOP) transfers substrates from Hsp70 to hsp 90.

2) co-chaperone activity (synonym of chaperone cofactor activity) co-chaperonin activity (obsolete) co-chaperones are proteins that bind to chaperones and the complex folds the misfolded proteins. Co-chaperones by themselves do not have chaperone activity. So gene products like GroES, also called co-chaperonin, should be annotated to chaperone cofactor activity. Some of them are nucleotide exchange factors also. Co-chaperones and co-chaperonins are used interchangeably. Consider protein binding and the process terms- chaperone_cofactor activity depedent protein folding

3) chaperonin ATPase activity (synonym) consider ATPase activity and the one of the protein folding process terms

4) glyco-protein specific chaperone activity (obsolete)- consider GO-process term N-linked glycoprotein maturation

5) tubulin-specific chaperone activity (obsolete) consider protein complex assembly/tubulin folding

6) fimbrium specific chaperone activity (obsolete) refers to proteins that assist in the linear organization of the protein pilus which forms the tubular structure or the organelle, fimbria (aka pilus) which helps bacteria attach to surface. These proteins are not involved in correcting the folding of pilus, they just help them come together. Consider : protein binding, bridging (GO-function) and fimbrium biogenesis process term. 7) chaperone inhibitor activity (obsolete)- Consider ATPase inhibitor activity, regulation of protein folding (proposing new term in process ontology) and its children terms 8) ribosomal chaperone activity- consider ribosome biogenesis 9) heat shock protein activity (obsolete), consider protein refolding process term 10) histone chaperone activity (obsolete): Consider histone binding, chromatin assembly/disassembly, nucleosome assembly 11)protein assembly, multchaperone pathway (obsolete)-consider one of the other protein assembly process terms.

In the following terms chaperone has been used to mean carrier/transport These terms have to be children/synonym of some transport term. 1) Copper chaperone activity synonym of copper ion tansporter activity, remove from chaperone activity node 2) Metallo chaperone activity synonym of metal ion transporter activity, remove from chaperone activity node 3) Superoxide dismutase copper chaperone activity (gene product ?obsolete?)- child of copper ion transporter activity, remove from chaperone activity node.

Original comment by: rbalakri

[gocentral]

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Hi Rama,

This looks good. 'holding chaperone activity' could probably be replaced by something else, too, actually; maybe something like 'protein binding' (with the substrate molecules annotated to 'chaperone binding') and a process term to describe what the chaperones are doing. It sounds like 'regulation of protein folding', possibly 'regulation of protein folding by holding chaperone'? You could use the standard regulation def and then add 'Holding chaperones hold or sequester macromolecules to prevent their aggregation or misfolding and is independent of nucleotide hydrolysis. Such substrate macromolecules attain their native conformation with the assistance of other chaperone molecules.' or something similar.

You don't need the underscores in the term names involving the chaperone cofactors.

Cheers, Amelia.

Original comment by: girlwithglasses

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Amelia,

How about a term called 'unfolded protein binding' as a child of protein binding in the function ontology?

Original comment by: rbalakri

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Yep, that would work.

Original comment by: girlwithglasses

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Hi amelia,

Yea!! Okay, here is a definition for 'unfolded protein binding activity'.

Refers to the activity of a class of protein molecules that bind unfolded or misfolded polypeptides.

thanks, Rama

Original comment by: rbalakri

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Rama, I would just use the standard 'binding' def for 'unfolded protein binding' - "Interacting selectively with an unfolded protein."

This looks ready to go now otherwise! :-)

Amelia.

Original comment by: girlwithglasses

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Hi Amelia,

Thanks. Yes, it is ready to go. I will try to commit them by the end of this week or sometime next week.

Rama

Original comment by: rbalakri

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Have done the following: New terms in the function ontology unfolded protein binding, GO:0051082 chaperone binding, GO:0051087

New terms in the process ontology cotranslational protein folding, GO:0051083 posttranslational protein folding, GO:0051084 chaperone cofactor dependent protein folding, GO:0051085 chaperone cofactor independent protein folding, GO:0051086

New obsoletes in the function ontology ribosomal chaperone activity, GO:0000005 chaperone activity, GO:0003754 glycoprotein-specific chaperone activity, GO:0003759 histone-specific chaperone activity, GO:0003762 co-chaperone activity, GO:0003767 co-chaperonin activity, GO:0003772 heat shock protein activity, GO:0003773 Hsp70/Hsp90 organizing protein activity, GO:0008077 fimbrium-specific chaperone activity, GO:0015472 tubulin-specific chaperone activity, GO:0017072

I would also like to obsolete the 'chaperone regulator activity' terms, so I'll leave this item open until their fate has been decided.

Original comment by: girlwithglasses

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Closing this item now but the chaperone regulator terms will be dealt with in due course, fear not!

Original comment by: girlwithglasses

[gocentral]

• labels: --> Other term-related request
• milestone: --> TermGenie
• status: open --> closed-fixed

Original comment by: girlwithglasses

[gocentral]

Hi All

looking at this record and records after this, there seems to be a general agreement that there will be a new chaperone activity within the 'Chaperone tree', but this seems to have got forgotten. This request is now 4 years old and the missing chaperone activity makes the ontology look very inconsistent. There are several terms refering to chaperone activity as if it is an accepted term such as chaperone binding, chaperone inhibitor etc. Please reinstate chaperone activity in some form to describe the activity of a protein which assists in the folding of other proteins.

Also below seems to suggest the term Protein binding %holding chaperone activity (new) would be created, but it has not appeared. However, I have no opinion on this one!)

Thanks

Ruth

Original comment by: RLovering