The distribution of different classes of nuclear localization signals (NLSs) in diverse organisms and the utilization of the minor NLS-binding site in plant nuclear import factor importin-alpha

The specific recognition between the import receptor importin-alpha and the nuclear localization signals (NLSs) is crucial to ensure the selective transport of cargoes into the nucleus. NLSs contain one or two clusters of positively-charged amino-acids, which usually bind to the major (monopartite NLSs) or both minor and major NLS-binding sites (bipartite NLSs). In our recent study, we determined the structure of importin-alpha 1a from rice (Oryza sativa), and made two observations that suggest an increased utilization of the minor NLS-binding site in this protein. First, unlike the mammalian protein, both the major and minor NLS-binding sites are auto-inhibited in the unliganded rice protein. Second, we showed that NLSs of the 'plant-specific' class preferentially bind to the minor NLS-binding site of rice importin-alpha. Here, we show that a distinct group of 'minor site-specific' NLSs also bind to the minor site of the rice protein. We further show a greater enrichment of proteins containing these 'plant-specific' and 'minor site-specific' NLSs in the rice proteome. However, the analysis of the distribution of different classes of NLSs in diverse eukaryotes shows that in all organisms, the minor site-specific NLSs are much less prevalent than the classical monopartite and bipartite NLSs.