Pore timing: the evolutionary origins of the nucleus and nuclear pore complex

. 2019 ; 8 () : . [epub] 20190403

Jazyk angličtina Země Velká Británie, Anglie Médium electronic-ecollection

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid31001417

Grantová podpora
MR/P009018/1 Medical Research Council - United Kingdom
MR/N010558/1 Medical Research Council - United Kingdom
203134/Z/16/Z Wellcome Trust - United Kingdom
R01 GM112108 NIGMS NIH HHS - United States
P41 GM109824 NIGMS NIH HHS - United States
R01 GM117212 NIGMS NIH HHS - United States
204697/Z/16/Z Wellcome Trust - United Kingdom

The name "eukaryote" is derived from Greek, meaning "true kernel", and describes the domain of organisms whose cells have a nucleus. The nucleus is thus the defining feature of eukaryotes and distinguishes them from prokaryotes (Archaea and Bacteria), whose cells lack nuclei. Despite this, we discuss the intriguing possibility that organisms on the path from the first eukaryotic common ancestor to the last common ancestor of all eukaryotes did not possess a nucleus at all-at least not in a form we would recognize today-and that the nucleus in fact arrived relatively late in the evolution of eukaryotes. The clues to this alternative evolutionary path lie, most of all, in recent discoveries concerning the structure of the nuclear pore complex. We discuss the evidence for such a possibility and how this impacts our views of eukaryote origins and how eukaryotes have diversified subsequent to their last common ancestor.

Zobrazit více v PubMed

Spang A, Caceres EF, Ettema TJG: Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science. 2017;357(6351): pii: eaaf3883. 10.1126/science.aaf3883 PubMed DOI

Leung KF, Dacks JB, Field MC: Evolution of the multivesicular body ESCRT machinery; retention across the eukaryotic lineage. Traffic. 2008;9(10):1698–716. 10.1111/j.1600-0854.2008.00797.x PubMed DOI

Rout MP, Field MC: The Evolution of Organellar Coat Complexes and Organization of the Eukaryotic Cell. Annu Rev Biochem. 2017;86:637–57. 10.1146/annurev-biochem-061516-044643 PubMed DOI

Dacks JB, Robinson MS: Outerwear through the ages: evolutionary cell biology of vesicle coats. Curr Opin Cell Biol. 2017;47:108–16. 10.1016/j.ceb.2017.04.001 PubMed DOI

Robinson MS: Forty Years of Clathrin-coated Vesicles. Traffic. 2015;16(12):1210–38. 10.1111/tra.12335 PubMed DOI

Field MC, Dacks JB: First and last ancestors: reconstructing evolution of the endomembrane system with ESCRTs, vesicle coat proteins, and nuclear pore complexes. Curr Opin Cell Biol. 2009;21(1):4–13. 10.1016/j.ceb.2008.12.004 PubMed DOI

Mosalaganti S, Kosinski J, Albert S, et al. : In situ architecture of the algal nuclear pore complex. Nat Commun. 2018;9(1): 2361. 10.1038/s41467-018-04739-y PubMed DOI PMC

Kosinski J, Mosalaganti S, von Appen A, et al. : Molecular architecture of the inner ring scaffold of the human nuclear pore complex. Science. 2016;352(6283):363–5. 10.1126/science.aaf0643 PubMed DOI PMC

Obado SO, Brillantes M, Uryu K, et al. : Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex. PLoS Biol. 2016;14(2):e1002365. 10.1371/journal.pbio.1002365 PubMed DOI PMC

Kim SJ, Fernandez-Martinez J, Nudelman I, et al. : Integrative structure and functional anatomy of a nuclear pore complex. Nature. 2018;555(7697):475–82. 10.1038/nature26003 PubMed DOI PMC

Alber F, Dokudovskaya S, Veenhoff LM, et al. : The molecular architecture of the nuclear pore complex. Nature. 2007;450(7170):695–701. 10.1038/nature06405 PubMed DOI

Rout MP, Aitchison JD, Suprapto A, et al. : The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol. 2000;148(4):635–51. 10.1083/jcb.148.4.635 PubMed DOI PMC

von Appen A, Kosinski J, Sparks L, et al. : In situ structural analysis of the human nuclear pore complex. Nature. 2015;526(7571):140–3. 10.1038/nature15381 PubMed DOI PMC

Beck M, Hurt E: The nuclear pore complex: understanding its function through structural insight. Nat Rev Mol Cell Biol. 2017;18(2):73–89. 10.1038/nrm.2016.147 PubMed DOI

Fischer J, Teimer R, Amlacher S, et al. : Linker Nups connect the nuclear pore complex inner ring with the outer ring and transport channel. Nat Struct Mol Biol. 2015;22(10):774–81. 10.1038/nsmb.3084 PubMed DOI

Teimer R, Kosinski J, von Appen A, et al. : A short linear motif in scaffold Nup145C connects Y-complex with pre-assembled outer ring Nup82 complex. Nat Commun. 2017;8(1): 1107. 10.1038/s41467-017-01160-9 PubMed DOI PMC

Lin DH, Stuwe T, Schilbach S, et al. : Architecture of the symmetric core of the nuclear pore. Science. 2016;352(6283):aaf1015. 10.1126/science.aaf1015 PubMed DOI PMC

Hayama R, Rout MP, Fernandez-Martinez J: The nuclear pore complex core scaffold and permeability barrier: variations of a common theme. Curr Opin Cell Biol. 2017;46:110–8. 10.1016/j.ceb.2017.05.003 PubMed DOI PMC

Jovanovic-Talisman T, Zilman A: Protein Transport by the Nuclear Pore Complex: Simple Biophysics of a Complex Biomachine. Biophys J. 2017;113(1):6–14. 10.1016/j.bpj.2017.05.024 PubMed DOI PMC

Holzer G, Antonin W: Nuclear Pore Complexes: Global Conservation and Local Variation. Curr Biol. 2018;28(11):R674–R677. 10.1016/j.cub.2018.04.032 PubMed DOI

Knockenhauer KE, Schwartz TU: The Nuclear Pore Complex as a Flexible and Dynamic Gate. Cell. 2016;164(6):1162–71. 10.1016/j.cell.2016.01.034 PubMed DOI PMC

Martin W, Koonin EV: Introns and the origin of nucleus-cytosol compartmentalization. Nature. 2006;440(7080):41–5. 10.1038/nature04531 PubMed DOI

Martin WF, Tielens AGM, Mentel M, et al. : The Physiology of Phagocytosis in the Context of Mitochondrial Origin. Microbiol Mol Biol Rev. 2017;81(3): pii: e00008-17. 10.1128/MMBR.00008-17 PubMed DOI PMC

Dey G, Thattai M, Baum B: On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype. Trends Cell Biol. 2016;26(7):476–85. 10.1016/j.tcb.2016.03.009 PubMed DOI PMC

Poole AM, Gribaldo S: Eukaryotic origins: How and when was the mitochondrion acquired? Cold Spring Harb Perspect Biol. 2014;6(12):a015990. 10.1101/cshperspect.a015990 PubMed DOI PMC

Yutin N, Wolf MY, Wolf YI, et al. : The origins of phagocytosis and eukaryogenesis. Biol Direct. 2009;4:9. 10.1186/1745-6150-4-9 PubMed DOI PMC

Pittis AA, Gabaldón T: Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry. Nature. 2016;531(7592):101–4. 10.1038/nature16941 PubMed DOI PMC

Dacks JB, Field MC, Buick R, et al. : The changing view of eukaryogenesis - fossils, cells, lineages and how they all come together. J Cell Sci. 2016;129(20):3695–703. 10.1242/jcs.178566 PubMed DOI

Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, et al. : Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature. 2017;541(7637):353–8. 10.1038/nature21031 PubMed DOI

Klinger CM, Spang A, Dacks JB, et al. : Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks. Mol Biol Evol. 2016;33(6):1528–41. 10.1093/molbev/msw034 PubMed DOI

Faini M, Beck R, Wieland FT, et al. : Vesicle coats: structure, function, and general principles of assembly. Trends Cell Biol. 2013;23(6):279–88. 10.1016/j.tcb.2013.01.005 PubMed DOI

Paraan M, Bhattacharya N, Uversky VN, et al. : Flexibility of the Sec13/31 cage is influenced by the Sec31 C-terminal disordered domain. J Struct Biol. 2018;204(2):250–60. 10.1016/j.jsb.2018.08.016 PubMed DOI PMC

Noble AJ, Zhang Q, O'Donnell J, et al. : A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry. Nat Struct Mol Biol. 2013;20(2):167–73. 10.1038/nsmb.2467 PubMed DOI PMC

Bykov YS, Schaffer M, Dodonova SO, et al. : The structure of the COPI coat determined within the cell. eLife. 2017;6: pii: e32493. 10.7554/eLife.32493 PubMed DOI PMC

Dodonova SO, Diestelkoetter-Bachert P, von Appen A, et al. : VESICULAR TRANSPORT. A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly. Science. 2015;349(6244):195–8. 10.1126/science.aab1121 PubMed DOI

Arakel EC, Schwappach B: Formation of COPI-coated vesicles at a glance. J Cell Sci. 2018;131(5): pii: jcs209890. 10.1242/jcs.209890 PubMed DOI

Devos D, Dokudovskaya S, Alber F, et al. : Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2004;2(12):e380. 10.1371/journal.pbio.0020380 PubMed DOI PMC

Devos D, Dokudovskaya S, Williams R, et al. : Simple fold composition and modular architecture of the nuclear pore complex. Proc Natl Acad Sci U S A. 2006;103(7):2172–7. 10.1073/pnas.0506345103 PubMed DOI PMC

Field MC, Koreny L, Rout MP: Enriching the pore: splendid complexity from humble origins. Traffic. 2014;15(2):141–56. 10.1111/tra.12141 PubMed DOI PMC

Field MC, Sali A, Rout MP: Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat. J Cell Biol. 2011;193(6):963–72. 10.1083/jcb.201102042 PubMed DOI PMC

Beck M, Mosalaganti S, Kosinski J: From the resolution revolution to evolution: structural insights into the evolutionary relationships between vesicle coats and the nuclear pore. Curr Opin Struct Biol. 2018;52:32–40. 10.1016/j.sbi.2018.07.012 PubMed DOI

Fath S, Mancias JD, Bi X, et al. : Structure and organization of coat proteins in the COPII cage. Cell. 2007;129(7):1325–36. 10.1016/j.cell.2007.05.036 PubMed DOI

Stuwe T, Lin DH, Collins LN, et al. : Evidence for an evolutionary relationship between the large adaptor nucleoporin Nup192 and karyopherins. Proc Natl Acad Sci U S A. 2014;111(7):2530–5. 10.1073/pnas.1311081111 PubMed DOI PMC

Sampathkumar P, Kim SJ, Upla P, et al. : Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure. 2013;21(4):560–71. 10.1016/j.str.2013.02.005 PubMed DOI PMC

Asakawa H, Yang HJ, Yamamoto TG, et al. : Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe. Nucleus. 2014;5(2):149–62. 10.4161/nucl.28487 PubMed DOI PMC

Tamura K, Fukao Y, Iwamoto M, et al. : Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. Plant Cell. 2011;22(12):4084–97. 10.1105/tpc.110.079947 PubMed DOI PMC

Iwamoto M, Osakada H, Mori C, et al. : Compositionally distinct nuclear pore complexes of functionally distinct dimorphic nuclei in the ciliate Tetrahymena. J Cell Sci. 2017;130(10):1822–34. 10.1242/jcs.199398 PubMed DOI PMC

DeGrasse JA, DuBois KN, Devos D, et al. : Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Mol Cell Proteomics. 2009;8(9):2119–30. 10.1074/mcp.M900038-MCP200 PubMed DOI PMC

Ori A, Banterle N, Iskar M, et al. : Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. Mol Syst Biol. 2013;9:648. 10.1038/msb.2013.4 PubMed DOI PMC

Cronshaw JM, Krutchinsky AN, Zhang W, et al. : Proteomic analysis of the mammalian nuclear pore complex. J Cell Biol. 2002;158(5):915–27. 10.1083/jcb.200206106 PubMed DOI PMC

Eibauer M, Pellanda M, Turgay Y, et al. : Structure and gating of the nuclear pore complex. Nat Commun. 2015;6:7532. 10.1038/ncomms8532 PubMed DOI PMC

Gomez-Cavazos JS, Hetzer MW: Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. Curr Opin Cell Biol. 2012;24(6):775–83. 10.1016/j.ceb.2012.08.008 PubMed DOI PMC

Raices M, D'Angelo MA: Nuclear pore complex composition: a new regulator of tissue-specific and developmental functions. Nat Rev Mol Cell Biol. 2012;13(11):687–99. 10.1038/nrm3461 PubMed DOI

D'Angelo MA: Nuclear pore complexes as hubs for gene regulation. Nucleus. 2018;9(1):142–8. 10.1080/19491034.2017.1395542 PubMed DOI PMC

Holden JM, Koreny L, Obado S, et al. : Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes. Mol Biol Cell. 2018;29(9):1100–10. 10.1091/mbc.E17-06-0430 PubMed DOI PMC

Obado SO, Field MC, Rout MP: Comparative interactomics provides evidence for functional specialization of the nuclear pore complex. Nucleus. 2017;8(4):340–52. 10.1080/19491034.2017.1313936 PubMed DOI PMC

Sakin V, Richter SM, Hsiao HH, et al. : Sumoylation of the GTPase Ran by the RanBP2 SUMO E3 Ligase Complex. J Biol Chem. 2015;290(39):23589–602. 10.1074/jbc.M115.660118 PubMed DOI PMC

Ritterhoff T, Das H, Hofhaus G, et al. : The RanBP2/RanGAP1*SUMO1/Ubc9 SUMO E3 ligase is a disassembly machine for Crm1-dependent nuclear export complexes. Nat Commun. 2016;7:11482. 10.1038/ncomms11482 PubMed DOI PMC

Szathmáry E, Smith JM: The major evolutionary transitions. Nature. 1995;374(6519):227–32. 10.1038/374227a0 PubMed DOI

O'Reilly AJ, Dacks JB, Field MC: Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. PLoS One. 2011;6(4):e19308. 10.1371/journal.pone.0019308 PubMed DOI PMC

Nejnovějších 20 citací...

Zobrazit více v
Medvik | PubMed

A lineage-specific protein network at the trypanosome nuclear envelope

. 2024 Dec ; 15 (1) : 2310452. [epub] 20240411

Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes

. 2023 Dec ; 98 (6) : 1910-1927. [epub] 20230619

Evolutionary, structural and functional insights in nuclear organisation and nucleocytoplasmic transport in trypanosomes

. 2023 Oct ; 597 (20) : 2501-2518. [epub] 20231015

Coatomer in the universe of cellular complexity

. 2022 Dec 01 ; 33 (14) : .

Evolution and diversification of the nuclear envelope

. 2021 Dec ; 12 (1) : 21-41.

Evolution and diversification of the nuclear pore complex

. 2021 Aug 27 ; 49 (4) : 1601-1619.

A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family

. 2021 Aug 03 ; 13 (8) : .

Evolution of late steps in exocytosis: conservation and specialization of the exocyst complex

. 2019 ; 4 () : 112. [epub] 20191129

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...