Chaperone children for obsoletion

[gocentral]

Here's another set of terms to be chaperoned to a new resting place under obsolete. Most of the terms describe a class of gene products via a combination of process and function information.

fimbrium-specific chaperone activity ; GO:0015472 (0 annotations) def: Assists in the correct assembly of fimbria, extracellular organelles that are used to attach a bacterial cell to a surface, but is not a component of the fimbrium when performing its normal biological function. -->chaperone ; GO:0003754 fimbrial biogenesis ; GO:0009297

plus a related obsoletion: fimbrial usher porin activity ; GO:0015473 def: A porin that acts in the assembly of fimbria together with fimbrial chaperone. -->porin ; GO:0015288 fimbrial biogenesis ; GO:0009297

glycoprotein-specific chaperone activity ; GO:0003759 (0 annotations) def: Assists in the correct, non-covalent assembly of glycoproteins in vivo, but is not a component of the assembled structures when performing its normal biological function. Utilizes a lectin site as a means to associate with the unfolded glycoproteins. -->just describes a specific type of protein; the lectin site is sequence info, not function. Can be merged into chaperone ; GO:0003754

heat shock protein activity ; GO:0003773 (196 annotations)

• Heat shock is a characteristic of a protein, not an activity; the activity remains chaperone. See email archive for previous discussion on this - http://www.geneontology.org/email/go-arc/go-2002/ 2614.html -->chaperone ; GO:0003754

histone-specific chaperone activity ; GO:0003762 (12 annotations) def: Assists in chromatin assembly by chaperoning histones on to replicating DNA, but is not a component of the nucleosome when performing its normal biological function. -->chaperone ; GO:0003754 DNA replication dependent nucleosome assembly ; GO:0006335

ribosomal chaperone activity ; GO:0000005 (2 annotations) def: Assists in the correct assembly of ribosomes or ribosomal subunits in vivo, but is not a component of the assembled ribosome when performing its normal biological function. -->chaperone ; GO:0003754 ribosome assembly ; GO:0042255

tubulin-specific chaperone activity ; GO:0017072 (5 annotations) def: Assists in the correct, non-covalent assembly of tubulin- containing structures in vivo, but is not a component of the assembled structures when performing its normal biological function. -->chaperone ; GO:0003754 chaperonin-mediated tubulin folding ; GO:0007022

co-chaperonin activity ; GO:0003772 is a gene product and should be obsoleted (as noted in SF:696664 - Rama is going to deal with this)

If there are no problems arising, these will be obsoleted on May 7th.

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/792":https://sourceforge.net/p/geneontology/ontology-requests/792

[gocentral]

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HI amelia,

As promised (remember from long time back) I have a draft have the chaperone activity tree. Can you please hold off on this? Most of the terms are going to go away based on my proposal.

thanks, rama

Original comment by: rbalakri

[gocentral]

• status: open --> open-postponed

Original comment by: girlwithglasses

[gocentral]

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=554736

----%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.

Original comment by: rbalakri

[gocentral]

• status: open-postponed --> closed-postponed

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796

Obsoleted the following: 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

See SF:869662 for the up-to-date version of this proposal.

Original comment by: girlwithglasses

[gocentral]

• status: closed-postponed --> closed-fixed

Original comment by: girlwithglasses