Modomics - A Database of RNA Modifications

Published on July 1, 2011 in RNA volume 17.

PubMed ID: 21628430


Pseudouridine (Psi), the isomer of uridine, is commonly found at various positions of noncoding RNAs of all organisms. Psi residues are formed by a number of single- or multisite specific Psi synthases, which generally act as stand-alone proteins. In addition, in Eukarya and Archaea, specific ribonucleoprotein complexes, each containing a distinct box H/ACA guide RNA and four core proteins, can produce Psi at many sites of different cellular RNAs. Cbf5 is the core Psi synthase in these complexes. Using Haloferax volcanii as an archaeal model organism, we show that, contrary to eukaryotes, the Cbf5 homolog (HVO_2493) is not essential in this archaeon. The Cbf5-deleted strain of H. volcanii completely lacks Psi at positions 1940, 1942, 2605, and 2591 (Escherichia coli positions 1915, 1917, 2572, and 2586) of its 23S rRNA, and contains reduced steady-state levels of some box H/ACA RNAs. Archaeal Cbf5 is known to have tRNA Psi55 synthase activity in vitro but we could not confirm this activity in vivo in H. volcanii. Conversely, the Pus10 (previously PsuX) homolog (HVO_1979), which can produce tRNA Psi55, as well as Psi54 in vitro, is shown here to be essential in H. volcanii, whereas the corresponding tRNA Psi55 synthases, Pus4 and TruB, are not essential in yeast and E. coli, respectively. Finally, we demonstrate that HVO_1852, the TruA/Pus3 homolog, is responsible for the pseudouridylation of position 39 in H. volcanii tRNAs and that the corresponding gene is not essential.

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