Sequence evidence for common ancestry of eukaryotic endomembrane coatomers

Abstract

Eukaryotic cells are defined by compartments through which the trafficking of macromolecules is mediated by large complexes, such as the nuclear pore, transport vesicles and intraflagellar transport. The assembly and maintenance of these complexes is facilitated by endomembrane coatomers, long suspected to be divergently related on the basis of structural and more recently phylogenomic analysis. By performing supervised walks in sequence space across coatomer superfamilies, we uncover subtle sequence patterns that have remained elusive to date, ultimately unifying eukaryotic coatomers by divergent evolution. The conserved residues shared by 3,502 endomembrane coatomer components are mapped onto the solenoid superhelix of nucleoporin and COPII protein structures, thus determining the invariant elements of coatomer architecture. This ancient structural motif can be considered as a universal signature connecting eukaryotic coatomers involved in multiple cellular processes across cell physiology and human disease.Nuclear pore complexes (NPCs) are modular assemblies embedded at the points of fusion between the inner and outer membrane of the eukaryotic nucleus that mediate nucleocytoplasmic transport 1 . The overall architecture and composition of the NPCs is largely taxonomically conserved, indicating early origins in the eukaryotic tree 2 . In particular, nucleoporins including those at the outer ring coat forming the Y-complex (outer ring coat Nups or Y-Nups) share certain key structural and architectural similarities, possibly due to deep divergence [3][4][5] . These features extend beyond the nuclear pore, namely the COPII coat associated with anterograde transport from the rough endoplasmic reticulum to the Golgi apparatus and the COPI coat associated with the reverse, retrograde transport 6 , suggesting a common origin of endomembrane coatomers, one class of which is represented by the NPC coat 7 . The divergence of nucleoporin families has been proposed on the basis of global structural but no specific sequence evidence, especially for the Y-Nups 8 . This presumption is based on detailed structural analysis, presence of beta-propeller repeats at the N-terminus, an alpha-solenoid superhelix at the C-terminus and other architectural elements with regard to the multi-domain composition of Y-Nups 5,9 . In particular, the solenoid superhelix of the resolved structures for Nup75, Nup96, Nup107 (Y-Nups) and Nic96 -reminiscent of the tetratrico-peptide repeat (TPR) domain 10 -is also present in Sec31 and Sec16, building blocks of the COPII vesicle coat 11,12 . Much attention has been paid to this structural element as a common architectural motif across diverse coatomer molecules, and has thus been named Ancestral Coatomer Element 1 (ACE1) 11,13 , favouring the hypothesis of deep divergence over convergent evolution14 . Yet, no sequence signature for ACE1 has ever been detected, either for Y-Nups/Nic96 or Sec31/Sec16, while the structure determination and comparison of these coatomers revealed this surprising structu...

Evolutionary divergence of the nuclear pore complex from fungi to metazoans

“…21 Recently, Ancestral Coatomer Element I (ACE1) was defined as the common architectural motif across diverse coatomer molecules thus defining both sequence and structural conserved motifs between the vesicle transport and nuclear pore complexes. 22 The fold analysis study of the S. cerevisiae Nups also shows that all the nucleoporins can be classified into seven classes which being α-helical, β-propeller, coiled coils, cadherin fold, RRM (RNA recognition motif ), autoproteolytic fold (hNup98), and the unstructured FG repeat regions. 23 These predicted fold types were assigned to nearly 28 Nups of S. cerevisiae which indicates that all of the Nups originated from a minimum set of precursor proteins by wide-ranging intragenic and intergenic duplications.…”