#10000 TPV: 90S preribosome assembly

closed-fixed
5
2013-02-22
2013-02-19
No

90S preribosome assembly, GO:0034463, is a part_of child of BOTH ribosomal small subunit assembly AND ribosomal large subunit assembly. We probably need two more specific terms:

90S preribosome assembly involved in ribosomal small subunit assembly
90S preribosome assembly involved in ribosomal large subunit assembly

and need to move the more generic term out.

Discussion

  • Karen Christie

    Karen Christie - 2013-02-20

    Hi Tanya,

    I spent some time in this area previously and have some comments.

    Basically, I do not think it would make sense to have two separate terms for
    "90S preribosome assembly involved in ..." small or large subunit assembly
    because at the time this is occurring, the small and large subunits do not exist
    separately, so there is only one process that can not be separated into one
    process for the large subunit and another one for the small. I should also
    comment that I am not sure how broadly applicable the "90S preribosome" is to
    all types of ribosome assembly. I know it occurs in yeast and mammals, but
    really don't know how broadly applicable it is to primary rRNA transcripts that
    are different from the 18S - 5.8S - 25S type found in yeast and mammals.

    The 90S preribosome assembles on the intact primary rRNA transcript and is
    intimately connected to the processing of the primary transcript into the 18S,
    25S, and 5.8S rRNAs. One of the things that happens within the 90S preribosome
    is the initial cleavage(s) that separate the primary transcript into the piece
    that will become the 18S that is in the small subunit and the piece that will
    become both the 25S and the 5.8S which are in the large subunit.

    While I'm looking at the tree, I have a couple related comments.

    1. I see that there is a separate term for "small-subunit processome assembly"
    (GO:0034462). My recollection is that "small subunit processome" and "90S
    preribosome" are synonyms, so I strongly suspect these should be merged. I think
    the "small-subunit processome" name is related to the fact that failure of the
    initial cleavage(s) of the rRNA primary transcript leads to failure in
    processing the 5'-end of the rRNA primary transcript that becomes the 18S rRNA
    and thus to loss of small subunits, but has little affect on large subunit
    production.

    2. The "maturation of 18S rRNA" (GO:1990041) looks like it was added subsequent
    to the reorganization of rRNA processing branch that Harold, Ceri, and I worked
    on a long time ago. One of the goals at that time was to get rid of as much of
    the xxS terminology as possible in primary term names. That turned out to be
    impossible for some of the small variant rRNAs found in non-mammalian
    eukaryotes, e.g. 2S rRNA, 4.5S rRNA. However, for the large and small subunit
    rRNAs, we wanted to make terms that did not use the xxS nomenclature because it
    is not completely consistent across species, e.g. I think the actual number is
    slightly different between cerevisiae andmammals. So, I think that the
    "maturation of 18S rRNA" term should be merged into this term:

    "maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" (GO:0000462)

    and then "maturation of 18S rRNA" should be a NARROW synonym. But, I'll get
    Harold to take a look at this second comment to make sure he agrees.

    thanks,

    Karen

     
  • Harold J. Drabkin

    Yes, we spent considerable time making sure we do not use "18" or "28" or 16, 23, etc. to describe the rRNAs due to species differences.
    I would merge the new term back in and of course, then "18s.... " would be a synonym

     
  • Tanya Berardini

    Tanya Berardini - 2013-02-20

    What bothered me was that '90S preribosome assembly' was part of both LSU and SSU assembly at the same time. However, any instance of 90S preribosome assembly will only be part of one of these, not both.

    If I merge "small subunit processome assembly" and "90S preribosome assembly" , shall I just drop the part_of relships to LSU assembly and SSU assembly and leave it as is_a 'ribonucleoprotein complex assembly'? Maybe part_of ribosome assembly? Given what you've said, that makes sense.

     
  • Karen Christie

    Karen Christie - 2013-02-21

    Hmmm, with respect to your comment that "any instance of 90S
    preribosome assembly will only be part of one of these, not both.", I
    would say that every individual "90S preribosome assembly" is relevant
    to both LSU and SSU assembly at the same time because the 90S
    preribosome represents the complex that forms on the primary rRNA
    transcript before it splits into the SSU and LSU portions. This view
    is supported by the Baserga lab review I include the citation for
    below.

    I also retract my suggestion to merge the 90S preribosome term with
    the SSU processome term. At the time I was working on this a few years
    ago, they seemed indistinguishable, but I thought I should check on
    current thought. Baserga, one of the main researchers on the SSU
    processome in cerevisiae, clearly thinks they are separate.

    Regarding relationships for the 90S preribosome term, I am not sure
    what is best. I was thinking about whether it works to just define the
    SSU and LSU assembly as starting after the 90S separates, but I don't
    think that works for the SSU. The 90S starts forming before the
    pre-rRNA transcript is complete, and it predominantly contains SSU
    factors, but it is not completely unrelated to LSU formation, as I
    understand it.

    Phipps KR, Charette J, Baserga SJ. The small subunit processome in ribosome
    biogenesis—progress and prospects. Wiley Interdiscip Rev RNA. 2011
    Jan-Feb;2(1):1-21. doi: 10.1002/wrna.57. Review. PubMed PMID: 21318072; PubMed
    Central PMCID: PMC3035417.

    -Karen

     
  • Tanya Berardini

    Tanya Berardini - 2013-02-21

    "... I would say that every individual "90S preribosome assembly" is relevant
    to both LSU and SSU assembly at the same time because the 90S
    preribosome represents the complex that forms on the primary rRNA
    transcript before it splits into the SSU and LSU portions. "

    But surely each instance of a 90S preribosome will only come part of either an LSU or a SSU but never both. For that reason, I think we should sever the part_of links to LSU and SSU assembly for 90S preribosome assembly. Replace with part_of ribosome assembly.

    -----------
    Separate issue. With Harold's agreement on your suggestion, I will merge "maturation of 18S rRNA" term into "maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8SrRNA, LSU-rRNA)" (GO:0000462) and keep shorter string as a narrow synonym.

     
  • Tanya Berardini

    Tanya Berardini - 2013-02-21

    I was just going to do the merge for the 18S term and noticed all its siblings:

    maturation of 2S rRNA
    maturation of 4.5S rRNA
    maturation of 5.8S rRNA
    maturation of 5S rRNA

    Are those ok as they are or do they need merging into something that doesn't state the size of S?

     
  • Tanya Berardini

    Tanya Berardini - 2013-02-21

    "Merge"maturation of 18S rRNA" term into "maturation of SSU-rRNA from
    tricistronic rRNA transcript (SSU-rRNA, 5.8SrRNA, LSU-rRNA)" (GO:0000462)
    and keep shorter string as a narrow synonym."

    Done.

     
  • Midori Harris

    Midori Harris - 2013-02-22

    Mind if I stick my oar in (decided to have a browse, since it's Friday afternoon )?

    > But surely each instance of a 90S preribosome will only come part of either
    > an LSU or a SSU but never both.

    But if I understand Karen's comments correctly, this actually isn't true. Each instance of 90S preribosome assembly makes a contribution to an instance of large subunit assembly AND an instance of small subunit assembly.

    That said, I've got no objection to having 90S preribosome assembly be just part_of ribosome assembly, especially if it's likely to make this part of the GO graph more intuitive.

    happy weekend,
    m

     
  • Tanya Berardini

    Tanya Berardini - 2013-02-22
    • status: open --> closed-fixed
     
  • Tanya Berardini

    Tanya Berardini - 2013-02-22

    AH! Sorry, Karen, for being slow. Thanks, Midori, for rewording. I've added to the def of that term to try to make that clear.

    New def: The aggregation, arrangement and bonding together of proteins and RNA molecules to form a 90S preribosome. The 90S preribosome represents the complex that forms on the primary rRNA transcript before it splits into the small subunit and large subunit portions.

    Leaving relationships as they are and closing this issue.

     

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