5 May 2015 PAINT Conference Call

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PAINT conference call minutes, May 5th, 2015

Participants:

Agenda and Minutes

Move PAINT repository off of sourceforge onto github

- There was an email sent out by Chris on April 27th. We should provide feedback how this should be handled for a smooth transition.

  • Karen: This is for the paint software and bug report on the sourceforge. It will not affect the SVN repository of paint curation (GAF) files. A while ago, the user guide was updated to this.
  • Moni: This is really to keep track of the bug report. Currently, the most recent bug report in SF is four years old.
  • Huaiyu: We then need to update the documentations on the paint working group wiki page. There is a PAINT sourceforge link on the page. It should be updated.

PAINT still writing "GO Central" instead of "GO_Central"(Karen)

  • The touch-up script corrects the term of "GO Central" to "GO_Central", but the PAINT software still writes "GO Central".
  • This was reported in the GitHub [see issue in GitHub]. Chris responded with a short perl script, which works.
  • Suzi needs to fix the PAINT software to make it consistent.

Family presentation PTHR23105(Karen)

Overview of the tree

This family contains the uL1 large ribosomal subunit sequences conserved across eubacteria (including chloroplast ribosomes), Archaea, and eukaryotes (including mitochondrial ribosomes) and also the eL8 large ribosomal subunit sequences conserved across Archaea and eukaryotes (aka yeast L8, mammalian L7A, Archaeal rpl7ae). There have been additional duplications in the eukaryotes producing proteins involved in ribosome biogenesis, but not present in the mature ribosome.

  • In Eubacteria, this tree contains:
    • uL1 (encoded by rplA sequences)
      Note: bacterial clade includes RPL1 genes encoding "50S ribosomal protein L1, chloroplastic"
  • In Archaea, this tree contains sequences for two ribosomal subunits:
    • uL1 (encoded by Archaeal rpl1p sequences; placement of rpl1p sequences is not consistent)
    • eL8 (encoded by Archaeal rpl7ae sequences)
  • In Eukaryea, this family includes
    • two cytosolic ribosomal subunits:
      • uL1 protein (RPL1A & RPL1B in S. cerevisiae), L10A in vertebrates (e.g. human RPL10A)
      • eL8 (aka yeast L8, mammalian L7A, Archaeal rpl7ae)
    • mitochondrial ribosomal subunits (encoded by MRPL1 genes)
    • RP related proteins involved in ribosome biogenesis, but not found in mature ribosome
      • UTP30 (aka RSL1D1 in vertebrates) in subclade with most of Archaeal rpl1p sequences
      • two proteins in subclade with eL8 sequences
        • NHP2
        • SNU13 (aka NHP2L1 in vertebrates)

Some issues in the tree

  • RSL1D1/UTP30 clade
    In addition to S.cerevisiae UTP30 and its E. gossypii homolog (Q756L8_ASHGO), this clade contains S.cerevisiae CIC1 and its E. gossypii homolog (Q75BL9_ASHGO), under a duplication node with just these two pairs of sequences. There aren't any other similar duplication nodes in this branch of the tree and the branch length to the CIC1 pair is greater than to the UTP30 pair. Looking at the full alignment, the Sc CIC1 and ASHGO_AGOS_AER236C (aka Q756L8_ASHGO) sequences look like they might be out of place, while the UTP30 and ASHGO_ACR252C pair looks pretty good.
    => I think I should probably prune these two sequences
  • MRPL1 clade
    • Yeast PLM2 and TOS4 sequences are paralogous transcription factors and do not belong in this tree
    • The G4VLH1_SCHMA is located most closely to the Yeast TOS4 sequence which does not belong in this tree, but it is annotated as "Putative 50s ribosomal protein L1" so I have left it here.

Annotations propagated

LUCA_PTN000559990

has function RNA binding (GO:0003723)
located in cytosolic large ribosomal subunit (GO:0022625)
participates in maturation of LSU-rRNA (GO:0000470)
participates in translation (GO:0006412)

Eukaryota_PTN000559994 = UTP30, aka RSL1D1

* lost/modified cytosolic large ribosomal subunit (GO:0022625) capacity
* lost/modified translation (GO:0006412) capacity

Eukaryota_PTN000560394 = NHP2

* lost/modified cytosolic large ribosomal subunit (GO:0022625) capacity
has function box H/ACA snoRNA binding (GO:0034513)
located in box H/ACA snoRNP complex (GO:0031429)
participates in snRNA pseudouridine synthesis (GO:0031120)
participates in rRNA pseudouridine synthesis (GO:0031118)
participates in cleavage involved in rRNA processing (GO:0000469)

Eukaryota_PTN000560317 = SNU13, aka NHP2L1

* lost/modified cytosolic large ribosomal subunit (GO:0022625) capacity
* lost/modified translation (GO:0006412) capacity
located in box C/D snoRNP complex (GO:0031428)
located in small-subunit processome (GO:0032040)
located in precatalytic spliceosome (GO:0071011)
located in U4/U6 x U5 tri-snRNP complex (GO:0046540)
participates in maturation of SSU-rRNA (GO:0030490)
participates in mRNA splicing, via spliceosome (GO:0000398)

Eukaryota_PTN001134767 = MRPL1 (mitochondrial RPL1)

* lost/modified cytosolic large ribosomal subunit (GO:0022625) capacity
located in mitochondrial large ribosomal subunit (GO:0005762)

Pruned from tree

  • Pruned YEAST_TOS4
  • Pruned YEAST_PLM2

Pictoral summary of the tree

PTHR23105-RP-L7AE-wNOTs.jpg