The modified base J is the target for a novel DNA-binding protein in kinetoplastid protozoans

DNA from Kinetoplastida contains the unusual modified base beta-D-glucosyl( hydroxymethyl)uracil, called J, Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes in Trypanosoma brucei. We have now identified a protein in nuclear extracts of bloodstream stage T.brucei that binds specifically t o J-containing duplex DNA, J-specific DNA binding was also observed with ex tracts from the kinetoplastids Crithidia fasciculata and Leishmania tarento lae, We purified the 90 kDa C.fasciculata J-binding protein 50000-fold and cloned the corresponding gene from C. fasciculata, T.brucei and L. tarentol ae, Recombinant proteins expressed in Escherichia coli demonstrated J-speci fic DNA binding. The J-binding proteins show 43-63% identity and are unlike any known protein. The discovery of a J-binding protein suggests that J, l ike methylated cytosine in higher eukaryotes, functions via a protein inter mediate.