RNA processing

[gocentral]

The names of the terms in the node 'RNA processing ; GO:0006396' need to be changed so that they don't contain sedimentation co-efficients i.e. need to be broad enough to apply to any organism - at the moment they're rather yeast-specific. The old names can be kept as synonyms. Also, defintions need to be added for all terms.

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/978":https://sourceforge.net/p/geneontology/ontology-requests/978

[gocentral]

Logged In: YES user_id=451873

Existing arrangement:

rRNA processing ; GO:0006364 < ribosome biogenesis ; GO:0007046 ---%35S primary transcript processing ; GO:0006365 ---%processing of 20S pre-rRNA ; GO:0030490 ---%processing of 27S pre-rRNA ; GO:0030489

None of these terms are defined.

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Proposed changes:

Name changes:

35S primary transcript processing -> large pre-rRNA transcript processing

processing of 20S pre-rRNA -> 20S class pre-rRNA processing

processing of 27S pre-rRNA -> 27S class pre-rRNA processing

Defintions:

rRNA processing Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule, for incorporation into a nascent ribosome.

large pre-rRNA transcript processing The processes by which the large precursor rRNA (pre-rRNA) is processed and cleaved into two smaller pre-rRNAs. In yeast the large transcript is 35S, and is cleaved into 20S and 27S pre-rRNAs, while in some mammals the large transcript is 45S and is cleaved into 20S and 32S pre-rRNAs. synonym: 35S primary transcript processing synonym: 45S pre-rRNA transcript processing

20S class pre-rRNA processing The processes by which the 20S, or equivalent pre-rRNA, is processed to form a mature 18S, or equivalent, rRNA molecule. synonym: 18S rRNA biosynthesis synonym: processing of 20S pre-rRNA

27S class pre-rRNA processing The processes by which the 27S, or equivalent pre-rRNA, is processed to form mature 25S and 5.8S, or equivalent, rRNA molecules. synonym: 25S and 5.8S rRNA biosynthesis synonym: processing of 27S pre-rRNA synonym: 32S class pre-rRNA processing

References: http://www.cell.com/content/article/fulltext?uid= PIIS0092867403004665 (PMID: 12837249) http://mcb.asm.org/cgi/content/full/19/12/7897?view=full&pmid= 10567516 (PMID: 10567516) http://www.sciencedirect.com/science?\_ob=ArticleURL&\_udi=B6VRW- 461X6DJ-B&_coverDate=06%2F01%2F2002&_alid=107339237& _rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6245&_sort=d&view= c&_acct=C000042238&_version=1&_urlVersion=0&_userid= 776054&md5=a2440d881f10cdd5035d79e90b1e889b (PMID: 12067653)

Original comment by: jl242

[gocentral]

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Existing arrangement:

rRNA processing ; GO:0006364 < ribosome biogenesis ; GO:0007046 ---%35S primary transcript processing ; GO:0006365 ---%processing of 20S pre-rRNA ; GO:0030490 ---%processing of 27S pre-rRNA ; GO:0030489

None of these terms are defined.

---

Proposed changes:

Name changes:

35S primary transcript processing -> large pre-rRNA transcript processing

processing of 20S pre-rRNA -> 20S class pre-rRNA processing

processing of 27S pre-rRNA -> 27S class pre-rRNA processing

Defintions:

rRNA processing Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule, for incorporation into a nascent ribosome.

large pre-rRNA transcript processing The processes by which the large precursor rRNA (pre-rRNA) is processed and cleaved into two smaller pre-rRNAs. In yeast the large transcript is 35S, and is cleaved into 20S and 27S pre-rRNAs, while in some mammals the large transcript is 45S and is cleaved into 20S and 32S pre-rRNAs. synonym: 35S primary transcript processing synonym: 45S pre-rRNA transcript processing

20S class pre-rRNA processing The processes by which the 20S, or equivalent pre-rRNA, is processed to form a mature 18S, or equivalent, rRNA molecule. synonym: 18S rRNA biosynthesis synonym: processing of 20S pre-rRNA

27S class pre-rRNA processing The processes by which the 27S, or equivalent pre-rRNA, is processed to form mature 25S and 5.8S, or equivalent, rRNA molecules. synonym: 25S and 5.8S rRNA biosynthesis synonym: processing of 27S pre-rRNA synonym: 32S class pre-rRNA processing

References: http://www.cell.com/content/article/fulltext?uid= PIIS0092867403004665 (PMID: 12837249) http://mcb.asm.org/cgi/content/full/19/12/7897?view=full&pmid= 10567516 (PMID: 10567516) http://www.sciencedirect.com/science?\_ob=ArticleURL&\_udi=B6VRW- 461X6DJ-B&_coverDate=06%2F01%2F2002&_alid=107339237& _rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6245&_sort=d&view= c&_acct=C000042238&_version=1&_urlVersion=0&_userid= 776054&md5=a2440d881f10cdd5035d79e90b1e889b (PMID: 12067653)

Original comment by: jl242

[gocentral]

Logged In: YES user_id=546388

There doesn't seem to be bacterial equivs in the rRNA processing tree. In bacteria, the large precursor is cleaved differently; Whereas in eukaryotes, the initial precursor is --18s--5.8S--28---, and the 5s is separate, in bacterial it is ---16s--23s--5s. (there is no 5.8s in bacteria). In addition to the three rRNAs, the precursor transcripts cointain variable lengths of spacer and one or more tRNA genes, depending upon which gene. for example, rrnA: --16s--tRNA(I)--tRNA(A)--23s--5s--

rrnB: --16s--tRNA(E)--23s--5s--

rrnC: --16s--tRNA(E)--23s--5s--tRNA(D)--tRNA(W)--

The first step in these instances is a cleavage that results in fragments that contain either a tRAN or a 16S,23S, or 5S rRNA sequence. This is done by RNase III. The extra nucleotides are then trimmed away, involving exonucleases that also perform the final step in triming in tRNA processing.

I suggest we add a sensu bacteria/prokaryote tree under rRNA processing to account for the different pathways.

Original comment by: hdrabkin

[gocentral]

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Why don't we just broaden the definition for 'large pre-rRNA transcript processing' to something like:

large pre-rRNA transcript processing The processes by which the large precursor rRNA (pre-rRNA) is processed and cleaved into smaller pre-rRNAs. In yeast the large transcript is 35S, and is cleaved into 20S and 27S pre-rRNAs, while in bacteria the large transcript is 30S, and is cleaved into three pre-rRNAs; 16S, 23S and 5S. synonym: 35S primary transcript processing synonym: 45S pre-rRNA transcript processing synonym: p30S RNA processing

and we can add some prokaryote-specific children. I don't like adding sensu terms unless they're really necessary...

Original comment by: jl242

[gocentral]

Logged In: YES user_id=546388

Just looked at this again; I know we don't like to but sensus in, but I think what we are going to need to do is create something like "pre-rRNA processing, sensu bacteria", and "pre-rRNA processing,. sensu eurkaryote" (or, "rRNA primary transcript processing, sensu etc.).The reason for this is that the primary transcript is differnet between the two from the very begining. We could then include in the defs the distinction. For children, we need to be careful because the order of steps (especially in bacteria), is not hard.

Original comment by: hdrabkin

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Hi,

This item has been open for a long time. Please comment to let us know whether you would like it to remain assigned to you, or would prefer it to be reassigned. (You don't necessarily have to work on it immediately if you keep it; we just need to know whether it's still on your list.)

Thanks, Midori & David Ontology development group managers

Original comment by: mah11

[gocentral]

Logged In: YES user_id=451873 Originator: YES

I'm going to unassign this one to myself - someone more knowlegable on RNA processing should take it over...

Jane

Original comment by: jl242

[gocentral]

• assigned_to: jl242 --> nobody

Original comment by: jl242

[gocentral]

Logged In: YES user_id=546388 Originator: NO

I talked to David on a related issue and to get rid of the sensu etc. we need to distinguish the ribosome type as being one whose ribosome has three processed RNAs (16, 23, 5) and four processed RNAs (5, 5.8, 18, 23).

Original comment by: hdrabkin

[gocentral]

Logged In: YES user_id=436423 Originator: NO

closing, now that the RNA processing working group has sorted things out. Those who have GOC wiki access can find more at http://gocwiki.geneontology.org/index.php/RNA\_processing.

Original comment by: mah11

[gocentral]

• status: open --> closed-fixed

Original comment by: mah11