def: mitochondrial RNA processing

[gocentral]

follow up to: http://sourceforge.net/tracker/index.php?func=detail&aid=1906309&group\_id=36855&atid=440764

compare the def of GO:0000965 ! mitochondrial RNA 3'-end processing [DEF: "Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome."]

with it's is_a parent: GO:0000959 ! mitochondrial RNA metabolic process [DEF: "The chemical reactions and pathways involving RNA in the mitochondrion."]

in the former, the condition is that the mRNA is derived from the mt genome. There is no constraint on the location at which the process unfolds.

In the latter, the condition is that the process takes place in the mt. There is no constraint on the derivational history of the mRNA.

This leaves the way open for two kinds of TPVs. I think only one of those is the more likely: mt genome transcribed RNA getting processed outside the mt. For example:

GO:0000172 ! ribonuclease MRP complex [DEF: "A ribonucleoprotein complex that performs the first cleavage in rRNA transcript processing and is also involved in mitochondrial RNA processing."]

As an aside, the following paper asserts that this is a snoRNP complex:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1369778

but it is not classified as such in GO. Perhaps because this itself would lead to TPVs? (through being located in the nucleolus)

I suggest that the defs of mt RNA metabolism and mt RNA processing terms are aligned

Reported by: cmungall

Original Ticket: "geneontology/ontology-requests/5195":https://sourceforge.net/p/geneontology/ontology-requests/5195

[gocentral]

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Biology issue here: for proteins, I know of only one process by which proteins can enter the mitochondrial matrix and none by which they can get out. I don't know of any process to move RNAs in either direction across the inner mt membrane (but my hunch, by analogy to the proteins, is that there isn't one). Evidence from an expert is badly needed here, but if there's no RNA traffic then the definitions can be narrowed to become consistent.

Peter

Original comment by: deustp01

[gocentral]

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Regarding your comment about MRP, here's what I know. For cerevisiae, I've seen MRP get classified by a snoRNA by the people who study snoRNAs. I've seen a number of reviews state that there are three families of snoRNAs: box C/Ds, box H/ACAs, and MRP, which is the sole representative of its class. However, it is clear that MRP had multiple functions.

Otherwise, I agree with Peter's comments about what can and cannot get out of the mitochondrion. As far as I'm aware any RNA produced in the mitochondrion is processed there and remains in the mitochondrion.

-Karen

Original comment by: krchristie

[gocentral]

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Thanks for the clarification. The logical xp definitions for these terms will use location as a differentium. See:

http://wiki.geneontology.org/index.php/XP:biological\_process\_xp\_cellular\_component\#mitochondrial\_X

(it would be good if the textual definition was unified. Perhaps this is low priority since the biological possibility of a TPV is low, and we can use the xps to generate textual defs later)

I'm still a little confused as to the location of ribonuclease MRP complex but I have little knowledge of this area and it sounds like things aren't conclusive anyway.

Original comment by: cmungall

[gocentral]

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I think that nuclear and mitochondrial MP should be separate terms, they have different composition:

Tracey H. Reilly1 and Mark E. Schmitt1 Abstract Ribonuclease P (RNase P) is a ribonucleoprotein responsible for the endonucleolytic cleavage of the 5-termini of tRNAs. Ribonuclease MRP (RNase MRP) is a ribonucleoprotein that has the ability to cleave both mitochondrial RNA primers presumed to be involved in mitochondrial DNA replication and rRNA precursors for the production of mature rRNAs. Several lines of evidence suggest that these two ribonucleoproteins are related to each other, both functionally and evolutionarily. Both of these enzymes have activity in the nucleus and mitochondria. Each cleave their RNA substrates in a divalent cation dependent manner to generate 5-phosphate and 3-OH termini. In addition, the RNA subunits of both complexes can be folded into a similar secondary structure. Each can be immunoprecipitated from mammalian cells with Th antibodies. In yeast, both have been found to share at least one common protein. This review will discuss some of the recent advances in our understanding of the structure, function and evolutionary relationship of these two enzymes in the yeast,Saccharomyces cerevisiae.

Original comment by: ValWood

[gocentral]

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Hi,

This is from the SGD summary paragraph from NME1, which encodes the RNA component of RNase MPR. It mentions that MRP is known to be found in both the nucleolus and the mitochondria in mammalian cells, while mitochondrial localization has not yet been shown in fungi.

http://db.yeastgenome.org/cgi-bin/locus.pl?locus=nme1\#summaryParagraph

Note: Three enzyme complexes involved in RNA processing are evolutionarily and physically related, and are easily confused with each other (see 16 and references therein). Mitochondrial RNase P is composed of the mitochondrially-encoded RPM1 RNA and the nuclear-encoded protein Rpm2p; it removes the 5' leaders from mitochondrial tRNA precursors. Nuclear RNase P, which removes the 5' leaders from cytoplasmic tRNA precursors, is composed of the RPR1 RNA subunit and Pop1p, Pop3p, Pop4p, Pop5p, Pop6p, Pop7p, Pop8p, Rpp1p, and Rpr2p. RNase MRP (RNase mitochondrial RNA processing) shares some subunits with nuclear RNase P: it is composed of an RNA subunit encoded by the nuclear NME1 gene and the protein subunits Rpp1p, Snm1p, Pop1p, Pop3p, Pop4p, Pop5p, Pop6p, Pop7p, Pop8p, and Rmp1p. RNase MRP processes pre-rRNAs in the nucleolus and is also present during mitosis in cytoplasmic RNA processing bodies, where it has a role in degradation of daughter cell-specific mRNAs via cleavage of 5' untranslated regions. In mammals, a portion of RNase MRP enters mitochondria and processes RNAs to create RNA primers for DNA replication, but this has not been shown in fungi.

Another comment for this def:

GO:0000172 ! ribonuclease MRP complex [DEF: "A ribonucleoprotein complex that performs the first cleavage in rRNA transcript processing and is also involved in mitochondrial RNA processing."]

It is NOT true that ribonuclease MRP performs the first cleavage, at least not universally. This would be more accurate, based on what I know now, though I'm going mostly on the paragraph which Maria Costanzo wrote for MRP in SGD.

GO:0000172 ! ribonuclease MRP complex [DEF: "A ribonucleoprotein complex that cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles. In S. cerevisiae it is cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication. PMID:14729943, PMID:7510714

-Karen

Original comment by: krchristie

[gocentral]

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I've made the mtRNA term defs more consistent and explicit. I also moved snoRNP complex up to is_a intracellular part so that MRP complex can be its is_a child; I added the nucleolar parentage back to the other children of snoRNA complex.

Thanks for all the comments, and for the improved def for GO:0000172 (which I've also put in). m

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11