Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122

Abstract

Importins ferry proteins into nuclei while exportins carry cargoes to the cytoplasm. In the accompanying paper in this issue (Vera Rodriguez et al. 2019. J. Cell Biol. https://doi.org/10.1083/jcb.201812091), we discovered that Pdr6 is a biportin that imports, e.g., the SUMO E2 ligase Ubc9 while depleting the translation factor eIF5A from the nuclear compartment. In this paper, we report the structures of key transport intermediates, namely, of the Ubc9•Pdr6 import complex, of the RanGTP•Pdr6 heterodimer, and of the trimeric RanGTP•Pdr6•eIF5A export complex. These revealed nonlinear transport signals, chaperone-like interactions, and how the RanGTPase system drives Pdr6 to transport Ubc9 and eIF5A in opposite directions. The structures also provide unexpected insights into the evolution of transport selectivity. Specifically, they show that recognition of Ubc9 by Pdr6 differs fundamentally from that of the human Ubc9-importer Importin 13. Likewise, Pdr6 recognizes eIF5A in a nonhomologous manner compared with the mammalian eIF5A-exporter Exportin 4. This suggests that the import of Ubc9 and active nuclear exclusion of eIF5A evolved in different eukaryotic lineages more than once and independently from each other.

Engineered SUMO/protease system identifies Pdr6 as a bidirectional nuclear transport receptor

“…This argues against redundancy in Ubc9 import and can be seen as a further specificity control. In the accompanying manuscript, we characterized the Ubc9-Pdr6 complex further and report its crystal structure (Aksu et al, 2019).…”

“…The functioning of the SUMO system thus requires a preset nucleocytoplasmic ratio in Ubc9 activity, and we now assume that such a gradient is best maintained by an active transport process. As discussed in the accompanying paper (Aksu et al, 2019), we regard it as an attractive possibility that Pdr6 also functions as a chaperone to modulate Ubc9 activity in a compartment-specific manner.…”

“…S4 C). In the case of eIF5A, it contacts both globular domains (see the accompanying paper by Aksu et al [2019] for a description of the structure); eEF2 lacks disordered regions that could possibly serve as a linear export signal. Therefore, Pdr6 appears to recognize folded domains.…”

Nucleocytoplasmic Shuttling of STATs. A Target for Intervention?

“…NTRs, also known as Karyopherins, can be subdivided in Importins and Exportins, facilitating nuclear import and export, respectively. Biportins have also been described that support transport of cargo in both directions with imported and exported cargo being distinct [14].…”

Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding

“…Recent extensive cargo or binding partner identifications failed to uncover novel consensus NLS/NES sequences 3 , 4 , 43 – 46 . Crystal structures of NTRs complexed with cargoes lacking the canonical NLS/NES have also been determined: Impβ 47 – 49 , Imp9 50 , Imp13 51 – 53 , Kap122p 54 , CSE1 55 , exportin-(Xpo)4 56 , Xpo5 57 , and Xpot 58 . In these structures, the NTRs interact with not just a short sequence of the cargo, but rather with multiple sites or a surface arranged conformationally, and respective cargoes bind to different positions on the NTRs.…”