Tales from the RNA Underworld - ESPs, Ancient Proteins and ancient RNA

EUKARYOTIC SIGNATURE PROTEINS - ANCIENT PROTEINS AND ANCIENT RNAS

Ok, so this isnt the ESP you were thinking of but it is still cool. 

Eukaryotic signature proteins (ESPs) are proteins that are present throughout eukaryotes (animals, plants, yeasts and protists), but not present in prokaryotes (bacteria and archaea). My PhD student Jian Han and I have been working on comparing these proteins between humans and some of their eukaryotic parasites (especially Giardia lamblia and Trichomonas vaginalis), to examine ancient similarities and differences between host and parasite. Although Giardia for example has a reduced genome (i.e. has kicked out all the genes it doesn’t need to use) it still retains all but one established ESP. We have also taken small RNA data from Giardia to look at possible miRNA regulation of ESPs.  It is becoming clearer that the ancestral eukaryote was not ‘primitive’ by any means having a complicated cellular structure and regulation to match. Our aim is to continue applying these insights in a medical way to help those who contact these rather uncomfortable diseases.

One of the ways we can analyse proteins and their interacting RNAs to to build networks indicating with nodes (circles) the protein or RNA and their connections (by the lines between them). These networks become complicated very very quickly and especially when we add in RNA-based regulation. However, when we look at the patterns within these large terrifying networks we can begin to see some trends in regulation. This is very much ongoing work with ESP and Spliceosomal RNA-protein networks. Stay tuned!