Protein Research Group, RIKEN genomic science center^* RIKEN Genomic Sciences Center, RIKEN SPring-8 Center Harima Institute^** RIKEN SPring-8 Center Harima Institute^*** RIKEN Genomic Sciences Center, RIKEN SPring-8 Center Harima Institute, The University of Tokyo^****
○Rie Shibata^* Yoshitaka Bessho^** Akeo Shinkai^*** Madoka Nishimoto^* Emiko Fusatomi^* Takaho Terada^** Mikako Shirouzu^** Shigeyuki Yokoyama^****

Many aspects of archaeal transcription are unknown, and especially, there is little evidence for termination mechanisms in archaea. Although the archaeal RNA polymerase (RNAP) more closely resembles the eukaryal RNAPs, bacterial transcription factor homologues are widely conserved in archaea. A homolog for bacterial transcription factor NusA is widely conserved in archaea. However, its function remained unknown since archaeal NusA consisted of only the two KH domains. In this study, we have found that Aeropyrum pernix NusA can strongly bind to a specific CU-rich sequence near a termination signal. This contrasts with its weak binding to the upstream portion of a hairpin region that reportedly interacts with bacterial NusA. Our crystal structure of A. pernix NusA suggests that its spatial arrangement is quite similar to that of the KH-domains of bacterial NusA. Remarkable differences between archaeal and bacterial NusA exist at the interface with RNAP. These evidences suggested that transcription termination in archaea is quite unique, as compared to all known bacterial and eukaryal termination systems, in terms of the use of the NusA transcription termination factor and a specific termination signal.