We isolated mouse cDNA clones (Arnt2) that are highly similar to but distinct from the aryl hydrocarbon receptor (AhR) nuclear translocator (Arnt). The composite cDNA covered a 2,443-bp sequence consisting of a putative 2,136-bp open reading frame encoding a polypeptide of 712 amino acids. The predicted Arnt2 polypeptide carries a characteristic basic helix-loop-helix (bHLH)/PAS motif in its N-terminal region with close similarity (81% identity) to that of mouse Arnt and has an overall sequence identity of 57% with Arnt. Biochemical properties and interaction of Arnt2 with other bHLH/PAS proteins were investigated by coimmunoprecipitation assays, gel mobility shift assays, and the yeast two-hybrid system. Arnt2 interacted with AhR and mouse Sim as efficiently as Arnt, and the Arnt2-AhR complex recognized and bound specifically the xenobiotic responsive element (XRE) sequence. Expression of Arnt2 successfully rescued XRE-driven reporter gene activity in the Arnt-defective c4 mutant of Hepa-1 cells. RNA blot analysis revealed that expression of Arnt2 mRNA was restricted to the brains and kidneys of adult mice, while Arnt mRNA was expressed ubiquitously. In addition, whole-mount in situ hybridization of 9.5-day mouse embryos showed that Arnt2 mRNA was expressed in the dorsal neural tube and branchial arch 1, while Arnt transcripts were detected broadly in various tissues of mesodermal and endodermal origins. These results suggest that Arnt2 may play different roles from Arnt both in adult mice and in developing embryos. Finally, sequence comparison of the currently known bHLH/PAS proteins indicates a division into two phylogenetic groups: the Arnt group, containing Arnt, Arnt2, and Per, and the AhR group, consisting of AhR, Sim, and Hif-1␣.The aryl hydrocarbon (Ah) receptor nuclear translocator (Arnt) is a member of a novel transcription factor family consisting of a basic helix-loop-helix (bHLH) structural motif contiguous with a PAS domain, a designated region conserved among Per (29, 38), Arnt (28), Ah receptor (AhR) (2, 13), and Sim (7, 34). Recent molecular cloning and biochemical studies have demonstrated that upon binding with an exogenous inducer such as 3-methylcholanthrene (3-MC) or 2,3,7,8-tetrachlorodibenzo-p-dioxin, the AhR is translocated from the cytoplasm to the nucleus. During this process, association of the AhR with heat shock protein 90 (HSP90) (8, 35, 52) is disrupted and a heterodimer with Arnt is formed (32, 40). The AhR-Arnt complex recognizes cis-acting DNA enhancer sequences, known as xenobiotic responsive elements (XREs), which function upstream of the cytochrome P-4501A1 (CYP1A1) gene to induce transcription (17,21). In addition to the induction of drug-metabolizing enzymes including CYP1A1, the AhR-Arnt system is considered to mediate the various biological effects of dioxin-like environmental pollutants, which include teratogenesis, tumor promotion, epithelial dysplasia, and immunosuppression (37,46,51). It has recently been reported that AhR gene disruption caused impairment of the li...