Scpl6Op (Succhuromyces cerevisiae protein involved in the control of ploidy), a polypeptide with a molecular mass of around 160 kDa, is associated with the nuclear envelope and the endoplasmic reticulum. The most noteworthy phenotype of SCP160 deletion mutants is a decrease in viability and an increased number of chromosomes in the surviving cells [Wintersberger, U., Kiihne, C. & Karwan, A. (1995) Yeast 11, 929-9441. Scpl6Op contains 14 KH domains, conserved motifs that have lately been identified in a variety of RNA-binding proteins. In this report, we demonstrate that the Scpl6Op sequence shows nearly perfect colinearity with the putative gene product of C08H9.2 from the nematode Cuenorhubditis elegans as well as with the vigilins, vertebrate RNA-binding proteins with a cellular location similar to that of Scpl6Op. Moreover, we found that Scpl6Op contains a potential nuclear-export signal (NES) near its N-terminus and a potential nuclear-localization signal (NLS) between KH domains 3 and 4. To determine whether the protein is able to bind to RNA, we purified Scpl6Op from yeast cell extract by DNA-cellulose and anti-Scpl6Op affinity chromatography. In northwestern blotting experiments, the electrophoretically homogeneous protein bound to ribohomopolymers and ribosomal RNA as well as to single-stranded and double-stranded DNA. Subcellular fractionation studies revealed that the major part of Scpl6Op is membrane associated via ionic interactions and can be released from the membrane fraction under conditions that lead to a dissociation of ribosomes. Together, our findings suggest that Scpl6Op is the yeast homologue of the vigilins, and point to a role for Scpl6Op in nuclear RNA export o r in RNA transport within the cytoplasm.Keywords: KH domain ; nucleic-acid-binding protein ; RNA transport.A multitude of RNA-binding proteins play key roles in the regulation of gene expression. Characterization of these proteins has led to the identification of several RNA-binding motifs [ 1, 21. One of these motifs, the KH domain (for K protein homology), was first identified as a repeated sequence in human hnRNP K protein [3]. According to secondary-structure prediction and NMR spectroscopy, the KH domain folds into a globular structure consisting of an antiparallel three-stranded P-sheet connected by two helical regions and an appended C-terminal helix [4]. Based on this secondary structure, it has been proposed that positively charged residues in the loop between the first two helices form a potential surface for contact with RNA [5] [I 8-20]. A direct in vivo interaction between the KH motif of ribosomal protein S3 and rRNA was demonstrated by cross-linking studies in 30s and 50s ribosomal subunits of E. coli and Bacillus stearothermophilus [9]. We have recently reported the cloning of SCP160 (S. cerevisiae gene involved in the control of ploidy). The gene, which is located on chromosome X, codes for a polypeptide with a molecular mass of around 160 kDa, Scpl6Op. Indirect immunofluorescence experiments with anti-Scpl60p ...