RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. 
DEAD-box helicases share a helicase core that mediates ATP binding and 
hydrolysis, RNA binding and unwinding. Most members of this family contain 
domains flanking the core that can confer RNA substrate specificity and guide 
the helicase to a specific RNA. However, the in vivo RNA substrates of most 
helicases are currently not defined. The DEAD-box helicase Hera from Thermus 
thermophilus contains a helicase core, followed by a dimerization domain and an 
RNA binding domain that folds into an RNA recognition motif (RRM). The RRM 
mediates high affinity binding to an RNA hairpin, and an adjacent duplex is then 
unwound by the helicase core. Hera is a cold-shock protein, and has been 
suggested to act as an RNA chaperone under cold-shock conditions. Using 
crosslinking immunoprecipitation of Hera/RNA complexes and sequencing, we show 
that Hera binds to a large fraction of T. thermophilus RNAs under normal-growth 
and cold-shock conditions without a strong sequence preference, in agreement 
with a structure-specific recognition of RNAs and a general function in RNA 
metabolism. Under cold-shock conditions, Hera is recruited to RNAs with high 
propensities to form stable secondary structures. We show that selected RNAs 
identified, including a set of tRNAs, bind to Hera in vitro, and activate the 
Hera helicase core. Gene ontology analysis reveals an enrichment of genes 
related to translation, including mRNAs of ribosomal proteins, tRNAs, tRNA 
ligases, and tRNA-modifying enzymes, consistent with a key role of Hera in 
ribosome and tRNA metabolism.