changes to vitelline membrane terms

[gocentral]

This stems from a SF query about taxon restrictions on the vitelline membrane terms: https://sourceforge.net/tracker/?func=detail&aid=3160726&group\_id=36855&atid=440764

Eggs in most organisms are surrounded by a protective layer (called the zone pellucid in mammals, and the vitelline membrane or vitelline envelope in non-mammals) (see PMID: 16944418).

egg envelope --zona pellucida (mammals) --vitelline membrane/envelope (non-mammals)

To allow querying across these egg envelopes, I'm proposing the following changes in GO. I'd appreciate it if organism-specific people (fly, mouse, fish and chickens) could take a look to see if it works for their organism. There's 3 parts: function, component and process.

1/ from: structural molecule activity ; GO:0005198 --[is_a]structural constituent of vitelline membrane ; GO:0008316 to: structural molecule activity ; GO:0005198 --[is_a]structural constituent of egg envelope ; GO:NEW1 ----[is_a]structural constituent of vitelline membrane ; GO:0008316 ----[is_a]structural constituent of zone pellucida ; GO:NEW2

structural constituent of egg envelope ; GO:NEW1 The action of a molecule that contributes to the structural integrity of the protective layer surrounding an egg. sensu restriction: Metazoa PMID: 16944418 PMID: 17163408 (InterPro:IPR005515 could get this term).

structural constituent of zone pellucida ; GO:NEW2 exact synonym: structural constituent of ZP The action of a molecule that contributes to the structural integrity of the zone pellucida, the specialized extracellular matrix that surrounds and protects the mammalian oocyte. sensu restriction: Mammalia PMID: 20662591

structural constituent of vitelline membrane ; GO:0008316. The action of a molecule that contributes to the structural integrity of the vitelline membrane, an envelope that surrounds and protects the oocytes of non-mammals. Examples of this are found in Drosophila, birds, amphibians and molluscs. PMID: 20457146. PMID: 18452232 new synonym: structural consistent of vitelline envelope (PMID: 16944418) sense restriction: NEVER_IN MAMMALIA.

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2/ from: external encapsulating structure --[is_a]vitelline envelope ; GO:0060388 to: external encapsulating structure --[is_a]egg envelope ----[is_a]vitelline envelope ; GO:0060388 ----[is_a]zona pellucida ; GO:NEW

egg envelope ; GO:NEW A protein-rich structure that lies outside the plasma membrane, and surrounds and protects the egg. PMID: 16944418 PMID: 17163408 sensu restriction: Metazoa (InterPro:IPR005515 could get this term).

zona pellucida ; GO:NEW A specialized extracellular matrix that surrounds and protects the mammalian oocyte. sensu restriction: Mammalia PMID: 20662591 MA:0001715

from: vitelline envelope ; GO:0060388 A glycoprotein-based structure that lies outside the plasma membrane and surrounds the egg before fertilization. related synonym: fertilization membrane to: vitelline membrane ; GO:0060388 A protein-rich structure that lies outside the plasma membrane, and surrounds and protects the egg of non-mammals. related synonym: fertilisation membrane exact synonym: vitelline envelope sense restriction: NEVER_IN MAMMALIA.

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3/ from: oogenesis ; GO:0030704 --[part_of]vitelline membrane formation ; GO:0030704 ----%vitelline membrane formation involved in chorion-containing eggshell formation ; GO:0007305

TO:

oogenesis ; GO:0030704 --[part_of]egg envelope formation ; GO:NEW ----[is_a]zona pellucida formation ; GO:NEW ----[is_a]vitelline membrane formation ; GO:0030704 ------[is_a]vitelline membrane formation involved in chorion-containing eggshell formation ; GO:0007305

egg envelope formation Construction of the egg envelope, a rigid structure required to protect and the egg, that plays a role in oogenesis, fertilization, and early development. PMID: 16944418 sensu restriction: Metazoa is_a: extracellular matrix assembly ; GO:0085029

zona pellucida formation ; GO:NEW Construction of the zone pellucida, a specialized extracellular matrix that surrounds and protects the mammalian oocyte. exact synonym: ZP assembly (PMID: 17566276) sensu restriction: Mammalia PMID: 20662591

vitelline membrane formation ; GO:0030704 from: Construction of the vitelline membrane portion of the egg shell, a rigid structure required to maintain the shape of the egg. TO: exact synonym: vitelline envelope Construction of the vitelline membrane, an envelope that surrounds and protects the oocytes of non-mammals. Examples of this are found in Drosophila, birds, amphibians and molluscs.

vitelline membrane formation involved in chorion-containing eggshell formation ; GO:0007305 (UNCHANGED… this is insect-specific) Construction of the vitelline membrane portion of a chorion-containing eggshell. An example of this is found in Drosophila melanogaster. sensu: Insecta

Q: is all egg envelope formation part of oogenesis? In some organisms, the envelope structure is changed upon fertilisation to prevent additional sperm entry.

Let me know if anything isn't clear. Thanks, Becky

Reported by: rebeccafoulger

Original Ticket: geneontology/ontology-requests/8097

[gocentral]

Well, I would really prefer to make all of the 'structural constituent of [some CC or anatomical structure]' terms obsolete, but I like all of the other suggestions.

m :)

Original comment by: mah11

[gocentral]

Given that several of these defs refers to the fact that the vitelline membrane/envelope/zona pellucida is an extracellular matrix should we add a relationship in cellular component to extracellular matrix GO:0031012 as well as to external encapsulating structure? Or could external encapsulating structure be a child of extracellular matrix?

Other than that I think the proposal is fine. Though I would have been tempted to lump them all together as a single 'egg envelope' terms with vitelline envelope, vitelline membrane and zona pellucida synonyms. The abstract of PMID: 17163408 highlights structural similarities between mouse and fish egg extracellular coats so I'm just wondering if there is a functional reason for lumping the non-mammalian structures together beyond the fact that they share 'vitelline' in the name for the structure? Don't have strong feelings either way. I'd prefer to keep the structural constituent terms though ;-)

I would say that all egg envelope formation is part of oogenesis and that any change in structure on fertilization is downstream of formation. Unless they don't have one at all prior to fertilization!

Original comment by: stweedie

[gocentral]

Fiona says:

My understanding is that the bird vitelline membrane separates the yolk from the egg white and roughly corresponds to the mammalian zona pellucida.This definition seems more geared for the membranes that surround the eggwhite. The structure of a chicken eggshell is: >From egg white - inner shell membrane outer shell membrane mamillary knobs pallisade layer cuticle

The eggshell itself is composed of the mamillary knobs (proteogylcan rich structures that start the mineralization process) and the pallisade layer of calcium carbonate within its organic matrix.

Let me check with my eggshell expert (!) and get back to you.

Original comment by: rebeccafoulger

[gocentral]

Created new broad egg coat terms: egg coat formation ; GO:0035803 structural constituent of egg coat ; GO:0035804 egg coat ; GO:0035805

Kept existing vitelline terms in all 3 ontologies for the moment, as children of the egg coat terms but haven't created any new specific terms.

Defined egg coat as: An egg coat is a specialized extracellular matrix that surrounds the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development.

thanks, Becky

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-works-for-me

Original comment by: rebeccafoulger