I am almost done building the structure of 80S ribosome from C.elegans, however I have run into a problem with one of the proteins form the large subunit .
I have clear density for a small protein, which in Yeast, drosophila and humans is called “L41” (for large ribosomal protein 41).
However I have not had any luck in identifying the protein in CE. I have tried blasting different versions of L41 (from the before mentioned organisms) against C.elegans or Caernorhabditis alone (taxID 6237) databases, but it yields nothing useful.
The protein is very small consisting of only 25 residues in both drosophila, yeast and human, and the density also indicates that it should be 23-25 residues long in CE. However the hits I get are of low similarity and originate from very large proteins that does not belong as part of the ribosome (at least not obviously), such as this one.
Does anyone here have an idea as to how I can identify this ribosomal protein so I can build it, or whom I could contact to get help with this problem maybe?
One thing to keep in mind is that you should probably be looking with a tblastn against the genome rather than a blastp against wormpep - the latter has certain biases, and omitting excessively short open reading frames is a huge one of them. It’s quite likely a 25 amino acid open reading frame would have been excluded.
Still, I didn’t find anything compelling with tblastn against the genome, and against ESTs the best I could find was /yk741g2, which I think isn’t right.
perhaps I fell asleep when someone was explaining why what I have dug out is wrong…but from a relatively well-known (well I know about it at least) database you find:
@Steveh: HA! one would think a structural ribosome guy like me would know about that database, but sadly I did not. And it looks like what you found, with what sounds like minimal effort, is exactly what I was looking for.
It seems I put to much faith in my beloved blastp searches, instead of looking for good alternative databases. You have helped me out before on this forum and now again, so I sincerely thank you for your help. Now the ribosome will look a bit better.
Your way to tell WormBase about gene curation issues seems to be perfectly fine.
Another variant would be to send an email to help@wormbase.org but the result is the same.
btw. I saw it in our tracker, so someone should come back to you soon
I’ve just curated the structure of F54D7.6, F54D7.7, following this discussion about them and the helpdesk message.
These two adjacent genes have erroneously been classified as pseudogenes.
I have now changed them to be coding genes.
The new structures will appear in database release WS251.
They produce identical tiny protein products (MREKWRKKRMRRLKRKRRAAKK) which are the C. elegans orthologs of the L41 protein in the S80 ribosomal complex.
I have notified our nomenclature expert that they should have a gene name in the ‘rpl’ gene class, but rpl-41 is already taken, so I do not yet know what they will be called.
the idea being that the same names are often used in different species for different (structurally and functionally) proteins.
The two L41s are interesting as they appear to be a duplication in C. elegans (separated by ~700bp). This is also the case for the paralogous L41A & L41B in S. cerevisiae (separated by ~100Kbp). Most other species appear to have only one (known) L41. Arabidopsis has several.
Anyway, perhaps the nomennclature team could draw inspiration from the above initiative?
great that you all work together on correcting what might seem like small insignificant errors!
Regarding the recent effort to standardise the ribosomal nomenclature, it is something I think a lot of ppl have wanted for a long time.
It is pretty difficult to navigate among ribosomal proteins from different organisms, as they are sometimes labeled almost arbitrarly. The L36/L36A/L41/L41.1/L41.2 in CE, is just one of those cases where it gets a bit confusing.
We are of course planning to publish our C.elegans 80S structure and I can guarantee that we will adhere to the standardised nomenclature as far as possible.
