Abstract
BackgroundMacromolecular transport across the nuclear envelope (NE) is achieved through nuclear pore complexes (NPCs) and requires karyopherin-βs (KAP-βs), a family of soluble receptors, for recognition of embedded transport signals within cargo. We recently demonstrated, through proteomic analysis of trypanosomes, that NPC architecture is likely highly conserved across the Eukaryota, which in turn suggests conservation of the transport mechanisms. To determine if KAP-β diversity was similarly established early in eukaryotic evolution or if it was subsequently layered onto a conserved NPC, we chose to identify KAP-β sequences in a diverse range of eukaryotes and to investigate their evolutionary history.ResultsThirty six predicted proteomes were scanned for candidate KAP-β family members. These resulting sequences were resolved into fifteen KAP-β subfamilies which, due to broad supergroup representation, were most likely represented in the last eukaryotic common ancestor (LECA). Candidate members of each KAP-β subfamily were found in all eukaryotic supergroups, except XPO6, which is absent from Archaeplastida. Phylogenetic reconstruction revealed the likely evolutionary relationships between these different subfamilies. Many species contain more than one representative of each KAP-β subfamily; many duplications are apparently taxon-specific but others result from duplications occurring earlier in eukaryotic history.ConclusionsAt least fifteen KAP-β subfamilies were established early in eukaryote evolution and likely before the LECA. In addition we identified expansions at multiple stages within eukaryote evolution, including a multicellular plant-specific KAP-β, together with frequent secondary losses. Taken with evidence for early establishment of NPC architecture, these data demonstrate that multiple pathways for nucleocytoplasmic transport were established prior to the radiation of modern eukaryotes but that selective pressure continues to sculpt the KAP-β family.
Highlights
The major defining feature of eukaryotic cells is the presence of a nucleus, the organelle that sequesters the genetic material away from the cytoplasm
For reasons of computational tractability, bootstrapped neighbour-joining (NJ) analysis was used to produce an initial subfamily classification system in which any sequences with similar BLAST results and located on adjacent branches of the NJ tree were counted as a cluster
BLAST analysis, we identified over six hundred KAP-b genes from a broad range of eukaryotes
Summary
The major defining feature of eukaryotic cells is the presence of a nucleus, the organelle that sequesters the genetic material away from the cytoplasm. This fundamental cellular architectural modification serves to compartmentalise transcription and translation and likely permitted the evolution of more complex mechanisms for regulating gene expression [1]. Active transport of protein and RNA is mediated by the karyopherin (KAP) family of nuclear transport receptors and the Ras-like GTPase Ran. There is a small family of KAP-as, six in Homo sapiens and one in Saccharomyces cerevisiae, which recognise nuclear localisation signals (NLS) on cargo and bind to a member of the larger KAP-b family [5]. To determine if KAP-b diversity was established early in eukaryotic evolution or if it was subsequently layered onto a conserved NPC, we chose to identify KAP-b sequences in a diverse range of eukaryotes and to investigate their evolutionary history
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