Simple fold composition and modular architecture of the nuclear pore complex

Damien Devos

Svetlana Dokudovskaya

Rosemary Williams

Frank Alber

*Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and California Institute for Quantitative Biomedical Research, University of California, Mission Bay QB3, 1700 4th Street, Suite 503B, San Francisco, CA 94143-2552; and Laboratories of

^{Cellular and Structural Biology and}

^{Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399}

^{To whom correspondence may be addressed. E-mail:}gro.balilas@ilas or ude.rellefekcor@tuor

Edited by Peter Walter, University of California School of Medicine, San Francisco, CA, and approved December 23, 2005

Author contributions: D.D., S.D., B.T.C., M.P.R., and A.S. designed research; D.D., S.D., and R.W. performed research; N.E. contributed new software; D.D., S.D., F.A., B.T.C., M.P.R., and A.S. analyzed data; and D.D., F.A., B.T.C., M.P.R., and A.S. wrote the paper.

Edited by Peter Walter, University of California School of Medicine, San Francisco, CA, and approved December 23, 2005

Received 2005 Jul 26

Abstract

The nuclear pore complex (NPC) consists of multiple copies of ≈30 different proteins [nucleoporins (nups)], forming a channel in the nuclear envelope that mediates macromolecular transport between the cytosol and the nucleus. With <5% of the nup residues currently available in experimentally determined structures, little is known about the detailed structure of the NPC. Here, we use a combined computational and biochemical approach to assign folds for ≈95% of the residues in the yeast and vertebrate nups. These fold assignments suggest an underlying simplicity in the composition and modularity in the architecture of all eukaryotic NPCs. The simplicity in NPC composition is reflected in the presence of only eight fold types, with the three most frequent folds accounting for ≈85% of the residues. The modularity in NPC architecture is reflected in its hierarchical and symmetrical organization that partitions the predicted nup folds into three groups: the transmembrane group containing transmembrane helices and a cadherin fold, the central scaffold group containing β-propeller and α-solenoid folds, and the peripheral FG group containing predominantly the FG repeats and the coiled-coil fold. Moreover, similarities between structures in coated vesicles and those in the NPC support our prior hypothesis for their common evolutionary origin in a progenitor protocoatomer. The small number of predicted fold types in the NPC and their internal symmetries suggest that the bulk of the NPC structure has evolved through extensive motif and gene duplication from a simple precursor set of only a few proteins.

Keywords: coated vesicle, protocoatomer, evolution, fold assignment

Abstract

The nuclear pore complex (NPC) is the only known selective gate for the passage of macromolecules across the nuclear envelope (NE) (1). The NPC is also one of the largest assemblies of defined structure in the cell, with a size of ≈50 MDa in yeast and up to 100 MDa in vertebrates. NPCs are common to all eukaryotes and are composed of a broadly conserved set of proteins termed nucleoporins (nups) (2) that have been fully cataloged for both yeast (3) and vertebrates (4).

Structural characterization of the whole NPC has proven challenging, because of its size and flexibility. A consensus low-resolution map of the NPC has emerged based largely on electron cryomicroscopy and tomography studies (5 –8). The NPC is a ring of eight identical spokes. Each spoke can be divided into almost identical cytosolic and nuclear half-spokes that each consist of ≈25 different nups (1). At the center of the NPC is an aqueous channel serving as the conduit for the transport of macromolecules. Macromolecular transport is regulated by the filamentous FG repeat-containing nups that emanate from the NPC into the nucleoplasm and cytoplasm. A comparison of the vertebrate and yeast NPCs reveals that the main features of the complex are conserved (1, 2).

Experimentally determined atomic structures are currently available for only seven nup fragments: ≈20 residues of the Nsp1 FxFG repeat region (9), 38 residues of the C terminus of Nup1 (10), a 6-residue FG-repeat segment of the CAN nup (the human homolog of Nup159) (11), the autocatalytic fragment of the vertebrate Nup98 (12), the equivalent 147-residue NPC-targeting domain at the C terminus of Nup116 (13), and the N-terminal domains of human Nup133 (14) and yeast Nup159 (15). Together, these domains represent a mere 5% of the total number of nup amino acid residues. Moreover, only an additional 5% of the residues can be related to proteins of known structure via statistically significant sequence similarity (Results); hence, there is a paucity of high-resolution structural data on nups.

Despite the central role of the NPC in the cell biology of all modern eukaryotes, there has been until recently little information concerning its origin and evolution in protoeukaryotes. To address this question, it would be helpful to have structural characterizations of many nups because it is easier to recognize similarities in structure than in sequence, especially for distantly related proteins. We recently used bioinformatics tools supported by limited proteolysis data to assign folds to domains in seven nups comprising the Nup84 subcomplex in yeast (16). These assignments allowed us to propose an evolutionary relationship between the Nup84 subcomplex of the NPC and coated vesicles (16), and other relationships have subsequently been suggested (17). In this work, we extend our previous analysis and assign folds for domains in all known nups, resulting in a structural characterization of ≈95% of the nup residues. We discuss the implications of these fold assignments for the structural organization and evolution of the NPC.

Shown are the number of residues in the corresponding nup sequence (size), an estimate of the domain range, the fold type of the corresponding model (where CC is coiled coil, FG is FG repeat, and Nup98 is the autocatalytic domain of Nup98), and Z scores of the comparative models (46) for the residues indicated in the parentheses. The predicted TMH, FG repeat, and coiled coil folds were not modeled. n.a., not applicable.

Click here to view.

Acknowledgments

We thank the members of the A.S. and M.P.R. laboratories for discussions about the NPC, especially Maya Topf and Fred Davis. We also thank Joe Fernandez and the Proteomic Resource Center of The Rockefeller University for protein sequence analysis. This work was supported by The Sandler Family Supporting Foundation, Sun Microsystems, IBM, Intel, and National Institutes of Health Grants GM62529 and GM54762 (to A.S.); by an Irma T. Hirschl Career Scientist Award, a Sinsheimer Scholar Award, a grant from the Rita Allen Foundation, and National Institutes of Health Grants GM062427 and RR022220 (to M.P.R.); and by National Institutes of Health Grants RR00862 (to B.T.C.) and CA89810 (to B.T.C. and M.P.R.).

Acknowledgments

Glossary

Abbreviations:

NPC	nuclear pore complex
NE	nuclear envelope
nup	nucleoporin
TMH	transmembrane helix
RRM	RNA recognition motif.

Glossary

Footnotes

Conflict of interest statement: No conflicts declared.

This paper was submitted directly (Track II) to the PNAS office.

Footnotes

References

1. Rout M. P., Aitchison J. D. J. Biol. Chem. 2001;276:16593–16596.[PubMed]
2. Suntharalingam M., Wente SR. Dev. Cell. 2003;4:775–789.[PubMed][Google Scholar]
3. Rout M. P., Aitchison J. D., Suprapto A., Hjertaas K., Zhao Y., Chait B. T. J. Cell Biol. 2000;148:635–651.
4. Cronshaw J. M., Krutchinsky A. N., Zhang W., Chait B. T., Matunis M. J. J. Cell Biol. 2002;158:915–927.
5. Beck M., Forster F., Ecke M., Plitzko JM., Melchior F., Gerisch G., Baumeister W., Medalia O. Science. 2004;306:1387–1390.[PubMed][Google Scholar]
6. Yang Q., Rout M. P., Akey C. W. Mol. Cell. 1998;1:223–234.[PubMed]
7. Jarnik M., Aebi U. J. Struct. Biol. 1991;107:291–308.[PubMed]
8. Stoffler D., Fahrenkrog B., Aebi U. Curr. Opin. Struct. Biol. 1999;11:391–401.[PubMed]
9. Bayliss R., Littlewood T., Stewart M. Cell. 2000;102:99–108.[PubMed]
10. Liu SM., Stewart M. J. Mol. Biol. 2005;349:515–525.[PubMed][Google Scholar]
11. Fribourg S., Braun IC., Izaurralde E., Conti E. Mol. Cell. 2001;8:645–656.[PubMed][Google Scholar]
12. Hodel A. E., Hodel M. R., Griffis E. R., Hennig K. A., Ratner G. A., Xu S., Powers M. A. Mol. Cell. 2002;10:347–358.[PubMed]
13. Robinson M. A., Park S., Sun Z.-Y. J., Silver P. A., Wagner G., Hogle J. M. J. Biol. Chem. 2005;280:35723–35732.[PubMed]
14. Berke I. C., Boehmer T., Blobel G., Schwartz T. U. J. Cell Biol. 2004;167:591–599.
15. Weirich C. S., Erzberger J. P., Berger J. M., Weis K. Mol. Cell. 2004;16:749–760.[PubMed]
16. Devos D., Dokudovskaya S., Alber F., Williams R., Chait B. T., Sali A., Rout M. P. PLoS Biol. 2004;2:e380.
17. Mans B. J., Anantharaman V., Aravind L., Koonin E. V. Cell Cycle. 2004;3:1612–1637.[PubMed]
18. McGuffin L. J., Jones D. T. Bioinformatics. 2003;19:874–881.[PubMed]
19. Przybylski D., Rost B. J. Mol. Biol. 2004;341:255–269.[PubMed]
20. Shi J., Blundell TL., Mizuguchi K. J. Mol. Biol. 2001;310:243–257.[PubMed][Google Scholar]
21. Soding J. Bioinformatics. 2005;21:951–960.[PubMed]
22. Koh I. Y., Eyrich V. A., Marti-Renom M. A., Przybylski D., Madhusudhan M. S., Eswar N., Grana O., Pazos F., Valencia A., Sali A., Rost B. Nucleic Acids Res. 2003;31:3311–3315.
23. Denning D. P., Patel S. S., Uversky V., Fink A. L., Rexach M. Proc. Natl. Acad. Sci. USA. 2003;100:2450–2455.
24. Saxena K., Gaitatzes C., Walsh M. T., Eck M., Neer E. J., Smith T. F. Biochemistry. 1996;35:15215–15221.[PubMed]
25. Fabre E., Hurt EC. Annu. Rev. Genet. 1997;31:277–313.[PubMed][Google Scholar]
26. Wheelock M. J., Johnson K. R. Annu. Rev. Cell Dev. Biol. 2003;19:207–235.[PubMed]
27. Strawn L. A., Shen T., Shulga N., Goldfarb D. S., Wente S. R. Nat. Cell Biol. 2004;6:197–206.[PubMed]
28. Lupas A. Methods Enzymol. 1996;266:513–525.[PubMed]
29. Fotin A., Cheng Y., Sliz P., Grigorieff N., Harrison SC., Kirchhausen T., Walz T. Nature. 2004;432:573–579.[PubMed][Google Scholar]
30. Marcotte E. M., Pellegrini M., Yeates T. O., Eisenberg D. J. Mol. Biol. 1999;293:151–160.[PubMed]
31. Wimmer C., Doye V., Grandi P., Nehrbass U., Hurt EC. EMBO J. 1992;11:5051–5061.[Google Scholar]
32. Wu J., Matunis MJ., Kraemer D., Blobel G., Coutavas E. J. Biol. Chem. 1995;270:14209–14213.[PubMed][Google Scholar]
33. Reverter D., Lima CD. Nature. 2005;435:687–692.[Google Scholar]
34. Conti E., Izaurralde E. Curr. Opin. Cell Biol. 2001;13:310–319.[PubMed]
35. Rabut G., Doye V., Ellenberg J. Nat. Cell Biol. 2004;6:1114–1121.[PubMed]
36. Loiodice I., Alves A., Rabut G., Van Overbeek M., Ellenberg J., Sibarita JB., Doye V. Mol. Biol. Cell. 2004;15:3333–3344.[Google Scholar]
37. Costas E., Goyanes V. Cytogenet. Genome Res. 2005;109:268–275.[PubMed]
38. Jacob F. Science. 1977;196:1161–1166.[PubMed]
39. McGuffin L. J., Bryson K., Jones D. T. Bioinformatics. 2000;16:404–405.[PubMed]
40. Kall L., Krogh A., Sonnhammer EL. J. Mol. Biol. 2004;338:1027–1036.[PubMed][Google Scholar]
41. Ward J. J., McGuffin L. J., Bryson K., Buxton B. F., Jones D. T. Bioinformatics. 2004;20:2138–2139.[PubMed]
42. Apweiler R., Bairoch A., Wu C. H., Barker W. C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., et al. Nucleic Acids Res. 2004;32:D115–D119.
43. Sali A., Blundell TL. J. Mol. Biol. 1993;234:779–815.[PubMed][Google Scholar]
44. Pearson WR. J. Mol. Biol. 1998;276:71–84.[PubMed][Google Scholar]
45. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Nucleic Acids Res. 1997;25:3389–3402.
46. Melo F., Sanchez R., Sali A. Protein Sci. 2002;11:430–448.
47. Dokudovskaya S. S., Williams R., Dews D., Sali A., Chait B. T., Rout M. P. Structure (London) 2006. in press. [PubMed]