Abstract
In eukaryotes, karyopherin beta superfamily proteins mediate nucleocytoplasmic transport of macromolecules. We investigated the evolutionary and transcriptional patterns of these proteins using bioinformatics approaches. No obvious homologs were found in prokaryotes, but an extensive set of beta-karyopherin proteins was found in yeast. Among 14 beta-karyopherins of Saccharomyces cerevisiae, eight corresponded to their human orthologs directly without diversification, two were lost, and the remaining four proteins exhibited gene duplications by different mechanisms. We also identified beta-karyopherin orthologs in Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Xenopus tropicalis, Gallus gallus, and Mus musculus. beta-Karyopherins were ubiquitously but nonuniformly expressed in distinct cells and tissues. In yeast and mice, the titer of some beta-karyopherin transcripts appeared to be regulated both during the cell cycle and during development. Further virtual analysis of promoter binding elements suggested that the transcription factors SP1, NRF-2, HEN-1, RREB-1, and nuclear factor Y regulate expression of most beta-karyopherin genes. These findings emphasize new mechanisms in functional diversification of beta-karyopherins and regulation of nucleocytoplasmic transport.
Highlights
In eukaryotes, karyopherin  superfamily proteins mediate nucleocytoplasmic transport of macromolecules
Putative binding sites of SP1, Nuclear respiratory factor 2 (NRF-2), helix protein 1 (HEN-1), Ras-responsive element-binding protein 1 (RREB-1), and nuclear factor Y (NF-Y) emerge frequently in upstream regions of -karyopherin genes in human and mouse, whereas Broad-complex serial binding sites are preferred in the fly (Table III and supplemental materials)
Bacteria do encode HEAT repeat proteins, such as CpcE and CpcF [36], the karyopherin  family itself appears to be absent from prokaryotes
Summary
Identification of Orthologous Proteins—The assignment of orthologous proteins is critical for evolutionary analyses of -karyopherins. Investigation of Regulatory Elements—400 bp of nucleotide sequences from Ϫ300 to ϩ100 bp of the transcript start of -karyopherin genes in eight species were derived from the Ensembl database [21] or GenBank for the transcription factor binding sites (TFBSs) analysis. To reduce the false positives, only species-specific TFBS models were adopted for predictions, e.g. TFBS models built from human, mouse, or fly data were only applied to human, mouse, or fly promoter sequences, respectively. These predictions were further combined with information on gene regulation to identify possible regulatory patterns
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