Nuclear import of proteins with nuclear localization signals (NLSs) is mediated by shuttling carriers, the importins. Some cargoes display more than a single NLS, and among these are homeodomain proteins such as Arx, which is critical for development of multiple tissues. Arx has two functional NLSs. The present studies show that several pathways can import Arx via its NLS2, which is within its DNA binding homeodomain. Using an in vitro nuclear import assay, we show that import of Arx via NLS2 can be mediated by importin 1, importin 9, or importin 13, with binding being strongest to importin 1. All binding is sensitive to RanGTP. Experiments based on precise domain deletions indicate that NLS2 binds imp1, imp9, and imp13 and includes both an importin binding subdomain and a regulatory subdomain with arginine residues being important for function. Moreover, Arx can be co-precipitated with these importins when NLS2 is present. Although nuclear import of Arx can be mediated by these three importin s, importin 1 seems to play the major role judging from in vivo small interfering RNA ablations and the in vitro import assay. This is the first evidence to show the role of importin 1 in nuclear import of paired-type homeodomain proteins. We propose a novel and possibly quite general mechanism for nuclear import of paired-type homeodomain proteins which is critical for development.Precise nucleocytoplasmic distribution of the homeodomain superfamily of transcription factors is critical for development. Several studies have demonstrated that NLS activity resides within the 60-amino acid DNA binding homeodomain itself, which is composed of three helices (1, 2). The "paired type" subgroup of the superfamily is characterized by a set of highly conserved residues. There are 26 members of this subgroup in man. The aristaless-related homeobox (ARX) 4 protein, a paired-type homeodomain containing protein, is mutated in multiple human conditions (3-5). ARX is expressed most strongly in the brain (6) and is important for development of the forebrain, pancreas, and testis (7). Arx proteins are highly conserved (Fig. 1) and contain 562 amino acids (564 amino acids in mouse) with four poly(A) (alanine) tracts of variable length, a paired-type homeodomain, and a conserved "aristaless" domain (8). Endogenous Arx was found in the nucleus of some types of nerve cells (9, 10). Because Arx has a molecular mass larger than 60 kDa, its nuclear import is likely to be signal-dependent. Three putative basic NLSs in Arx have been proposed (8, 11): NLS1 from aa 82 to 89, BC1 from aa 327 to 334, and BC2 from aa 381 to 388 (Fig. 1). It is not clear whether or how these putative NLSs function in the nuclear localization of Arx.As for other trinucleotide-repeat-containing genes (12, 13), the first poly(A) tract can expand in Arx. Expansion of this tract or loss of the 3Ј aristaless domain in Arx are both associated with infantile spasms syndrome and mental retardation (14, 15). Moreover, expansion of the first poly(A) tract of Arx results in for...