I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?

Phylogentic tree

  • $\begingroup$ It's looking an interesting question. Can you kindly add bit more details? $\endgroup$ – Failed Scientist Mar 26 at 9:20
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    $\begingroup$ Welcome to SE Biology. Please complete the Tour to find out how this site works. Also read about how to ask questions. It is unclear whether you want are appealing for someone to do your work for you (definitely not the purpose of this site) or information on how to go about it. Assuming the latter, it is impossible to help you without knowing what your gene is. If your Blast search is bringing up PPIs, then I would imagine your gene is a PPI. Show us the sequence comparison, not the tree. $\endgroup$ – David Mar 26 at 13:03
  • $\begingroup$ I have edited your question to correspond to what I think your problem is and have provided an answer. If you disagree, you can revert the question but you would need to clarify it. I hope I have not inadvertently answered an assignment rather than a real research problem. If this was a real research problem, you would be advised to believe the evidence of your own analysis in future, and do some research on what they bring up. $\endgroup$ – David Mar 26 at 16:20

Without seeing the sequence of the RNA-binding protein it is impossible to be sure, but the obvious conclusion is:

The RNA-binding protein is a peptidyl-prolyl cis-trans isomerase.

It has been known since 1989 that peptidyl-prolyl cis-trans isomerase is a multiple-function protein, also exhibiting properties of the cyclophilins, proteins which bind cyclosporin A. The post raised the possibility that it may have other activities and a literature search reveals several more recent papers that indicate cylcophilin A can bind certain RNAs. I list some of the titles:

A nuclear RNA-binding cyclophilin in human T cells (1996) FEBS Letters 398 201–205

Molecular cloning, structure and expression of a novel nuclear RNA-binding cyclophilin-like gene (PPIL4) from human fetal brain (2001) Cytogenet Cell Genet 95 43–47

Cyclophilin A Binds to the Viral RNA and Replication Proteins, Resulting in Inhibition of Tombusviral Replicase Assembly (2013) J. Virol. 87 13330–13342

Structure of RNA-interacting Cyclophilin A-like protein from Piriformospora indica that provides salinity-stress tolerance in plants (2013) Scientific Reports 3 : 3001, DOI: 10.1038/srep03001

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