Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEADprotein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins

DEAD, DEAH and DExH proteins are involved in almost every facet of RNA bioc hemistry. Members of these protein families exhibit an RNA-dependent ATPase activity and some possess an ATP-dependent RNA helicase activity. Although genetic studies have identified specific functions for certain DEx(H)(D/) proteins from which an RNA substrate can be reasonably inferred, only DbpA from Escherichia coil has been shown to exhibit significant RNA specificity in vitro. Here we describe the characterization of YxiN from Bacillus subt ilis, the second DEx(H)(D/) protein to show significant RNA specificity as an isolated, homogenous protein. The ATPase activity of YxiN, like that of DbpA, is stimulated by a 154 nt fragment of 23S rRNA, YxiN has a 2 nM appar ent binding constant for this fragment, yet its ATPase activity shows 1800- fold RNA specificity. Along with the conserved motifs shared among all DEAD proteins, YxiN and DbpA have a conserved C-terminal extension, This extens ion is highly conserved in several additional DEAD proteins, We propose tha t the C-terminus identifies a protein sub-family whose members bind 23S rRN A and that proteins of this family are likely to function in rRNA maturatio n/ribosome biogenesis or an unappreciated aspect of translation.