Obsoletion request: GO:1990124 messenger ribonucleoprotein complex

[ValWood]

Please provide as much information as you can:

• GO term ID and Label

• Reason for deprecation Put an x in the appropriate box:

  • [x] The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.

(There are no descendent terms)

• "Consider" term(s) (ID and label) Suggestions for reannotation

Quick scan of the annotations - these could move to the various correct specific complex term in most cases

More explanation of why it is a problem term below.

• Are there annotations to this term?
• How many EXP: 44

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Checklist for ontology editor

Check term usage and metadata in Protégé

• [ ] check term usage in the ontology
• [ ] check internal mappings: RHEA, EC, MetaCyc
• [ ] check subset usage
• [ ] check taxon constraints

Check annotations

• [x] https://github.com/geneontology/go-annotation/issues/4920
• [x] find external mappings (via IEAS), include in obsoletion notice

Notification

• [x] create obsoletion announcement
• [ ] announce to GO friends (go-friends@mailman.stanford.edu)
• [ ] paste the text in the ontology ticket

[ValWood]

@pgaudet do you agree? (no hurry, I have lots in progress)

[pgaudet]

I dont have strong opinions about complexes, but that seems to be used in the iterature? https://pubmed.ncbi.nlm.nih.gov/?term=mRNP+complex

[ValWood]

This isn't a specific complex though, and it's used inconsistently.

If I quote the "mRNP complex" I get fewer hits

https://pubmed.ncbi.nlm.nih.gov/?term=%22mRNP+complex%22&sort=date&size=50

referring to different entities. Usually used as a generic grouping term.

In GO it is defined A ribonucleoprotein complex containing both protein and messenger RNA (mRNA) molecules. PMID:15574591 PMID:21915786

which could be anything, and consequently it is used to annotate random things, including elongation factor, or anything that binds to a mRNA

FyBase have used it a bit so tagging @hattrill to see if this is meant to refer to a specific complex, because if it is, it should have a more precise definition.

Note that it isn't a grouping term in GO, it has no descendants, so it seems that it should refer to a specific complex.

[hattrill]

@ValWood think that we can live without this term - just a handful of annotations to review and if we need specific terms, I will request. As it has no children and is vague, I am pro obsoletion.

[ValWood]

This is what it means:

CPC-CHAT The messenger ribonucleoprotein (mRNP) complex refers to a complex structure formed by messenger RNA (mRNA) molecules and associated proteins within the cell. mRNA is a molecule that carries genetic information from the DNA in the cell's nucleus to the ribosomes, where proteins are synthesized.

The mRNP complex is crucial for various processes involved in gene expression, including mRNA processing, transport, localization, stability, and translation. It is composed of mRNA molecules bound to numerous proteins that help regulate and facilitate the different stages of mRNA's life cycle within the cell.

These associated proteins within the mRNP complex can include:

RNA-binding proteins: These proteins interact with specific sequences or structures on the mRNA molecule, affecting its stability, localization, and translation.

Splicing factors: They assist in the removal of non-coding sequences (introns) from the mRNA precursor (pre-mRNA) during mRNA processing called splicing.

Transport proteins: They aid in transporting mRNA molecules from the cell nucleus to the cytoplasm, where translation occurs.

Regulatory proteins: These proteins can control mRNA stability, localization, or translation efficiency, impacting gene expression levels.

The composition and dynamics of the mRNP complex play a significant role in modulating gene expression, allowing the cell to regulate protein production in response to various internal and external cues. Dysfunction or alterations in the mRNP complex can lead to disruptions in gene expression, potentially contributing to various diseases or developmental disorders.

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so it isn't really describing a single complex but everything that occurs associated with any mRNA molecule (and essentially 100's of proteins'. It isn't really possible to describe this complexity as a single term in GO.

Its more of a "composite" concept for everything happening to the transcriptional and translations unit. synonymous with https://en.wikipedia.org/wiki/Messenger_RNP

[ValWood]

I didn't tag wormbase... @vanaukenk could you look at yours? 5 annotations. Thanks!

[vanaukenk]

@ValWood

WB annotations done

[ValWood]

All annotations removed, process to obsoletion