The β-propeller protein Sec13 plays roles in at least three distinct processes by virtue of being a component of the COPII endoplasmic reticulum export vesicle coat, the nuclear pore complex (NPC) and the Seh1-associated (SEA)/GATOR nutrient-sensing complex. This suggests that regulatory mechanisms coordinating these cellular activities may operate via Sec13. The NPC, COPII and SEA/GATOR are all ancient features of eukaryotic cells, and in the vast majority of eukaryotes, a single Sec13 gene is present. Here we report that the Euglenozoa, a lineage encompassing the diplonemid, kinetoplastid and euglenid protists, possess two Sec13 paralogues. Furthermore, based on protein interactions and localization studies we show that in diplonemids Sec13 functions are divided between the Sec13a and Sec13b paralogues. Specifically, Sec13a interacts with COPII and the NPC, while Sec13b interacts with Sec16 and components of the SEA/GATOR complex. We infer that euglenozoan Sec13a is responsible for NPC functions and canonical anterograde transport activities while Sec13b acts within nutrient and autophagy-related pathways, indicating a fundamentally distinct organization of coatomer complexes in euglenozoan flagellates.

Centre for Life's Origins and Evolution Department of Genetics Evolution and Environment University College London London UK

Division of Infectious Diseases Department of Medicine Faculty of Medicine and Dentistry University of Alberta Edmonton Canada

Faculty of Science Charles University BIOCEV Vestec Czech Republic

Faculty of Sciences University of South Bohemia České Budějovice Czech Republic

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czech Republic

Life Science Research Centre Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic

School of Life Sciences University of Dundee Dundee UK

Zobrazit více v PubMed

Dacks JB, Field MC. 2007. Evolution of the eukaryotic membrane-trafficking system: Origins, tempo and mode. J. Cell Sci. 120, 2977-2985. (10.1242/jcs.013250) PubMed DOI

Wideman JG, Muñoz-Gómez SA. 2016. The evolution of ERMIONE in mitochondrial biogenesis and lipid homeostasis: an evolutionary view from comparative cell biology. Biochim. Biophys. Acta—Mol. Cell Biol. Lipids 1861, 900-912. (10.1016/j.bbalip.2016.01.015) PubMed DOI

Dacks JB, Field MC. 2018. Evolutionary origins and specialisation of membrane transport. Curr. Opin. Cell Biol. 53, 70-76. (10.1016/j.ceb.2018.06.001) PubMed DOI PMC

Rutherford S, Moore I. 2002. The Arabidopsis Rab GTPase family: another enigma variation. Curr. Opin. Plant Biol. 5, 518-528. (10.1016/S1369-5266(02)00307-2) PubMed DOI

Carlton JM, et al. 2007. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315, 207-212. (10.1126/science.1132894) PubMed DOI PMC

Neumann N, Lundin D, Poole AM. 2010. Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PLoS ONE 5, e13241. (10.1371/journal.pone.0013241) PubMed DOI PMC

Rout MP, Field MC. 2022. Coatomer in the universe of cellular complexity. Mol. Biol. Cell 33, pe8. (10.1091/mbc.e19-01-0012) PubMed DOI PMC

Schlacht A, Dacks JB. 2015. Unexpected ancient paralogs and an evolutionary model for the COPII coat complex. Genome Biol. Evol. 7, 1098-1109. (10.1093/gbe/evv045) PubMed DOI PMC

Vargová R, Wideman JG, Derelle R, Klimeš V, Kahn RA, Dacks JB, Eliáš M. 2021. A eukaryote-wide perspective on the diversity and evolution of the ARF GTPase protein family. Genome Biol. Evol. 13, evab157. (10.1093/gbe/evab157) PubMed DOI PMC

Tang BL. 2017. Sec16 in conventional and unconventional exocytosis: working at the interface of membrane traffic and secretory autophagy? J. Cell. Physiol. 232, 3234-3243. (10.1002/jcp.25842) PubMed DOI

Yorimitsu T, Sato K. 2020. Sec16 function in ER export and autophagy is independent of its phosphorylation in Saccharomyces cerevisiae. Mol. Biol. Cell 31, 149-156. (10.1091/mbc.E19-08-0477) PubMed DOI PMC

Fontoura BMA, Blobel G, Matunis MJ. 1999. A conserved biogenesis pathway for nucleoporins: proteolytic processing of a 186-kilodalton precursor generates Nup98 and the novel nucleoporin, Nup96. J. Cell Biol. 144, 1097-1112. (10.1083/jcb.144.6.1097) PubMed DOI PMC

Dokudovskaya S, et al. 2011. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol. Cell. Proteomics 10, M110.006478. (10.1074/mcp.M110.006478) PubMed DOI PMC

Loissell-Baltazar YA, Dokudovskaya S. 2021. SEA and GATOR 10 years later. Cells 10, 2689. (10.3390/cells10102689) PubMed DOI PMC

Barlowe C, et al. 1994. COPII: a membrane coat formed by Sec proteins that drive vesicle budding from the endoplasmic reticulum. Cell 77, 895-907. (10.1016/0092-8674(94)90138-4) PubMed DOI

Flegontova O, Flegontov P, Londoño PAC, Walczowski W, Šantić D, Edgcomb VP, Lukeš J, Horák A. 2020. Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans. Environ. Microbiol. 22, 4014-4031. (10.1111/1462-2920.15190) PubMed DOI

Prokopchuk G, Korytář T, Juricová V, Majstorović J, Horák A, Šimek K, Lukeš J. 2022. Trophic flexibility of marine diplonemids—switching from osmotrophy to bacterivory. ISME J. 16, 1409-1419. (10.1038/s41396-022-01192-0) PubMed DOI PMC

Tashyreva D, et al. 2022. Diplonemids—a review on ‘new’ flagellates on the oceanic block. Protist 173, 125868. (10.1016/j.protis.2022.125868) PubMed DOI

Faktorová D, et al. 2020. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat. Methods 17, 481-494. (10.1038/s41592-020-0796-x) PubMed DOI PMC

Faktorová D, Kaur B, Valach M, Graf L, Benz C, Burger G, Lukeš J. 2020. Targeted integration by homologous recombination enables in situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum. Environ. Microbiol. 22, 3660-3670. (10.1111/1462-2920.15130) PubMed DOI

Valach M, et al. 2023. Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes. BMC Biol. 21, 99. (10.1186/s12915-023-01563-9) PubMed DOI PMC

Kaur B, Záhonová K, Valach M, Faktorová D, Prokopchuk G, Burger G, Lukeš J. 2020. Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids. Nucleic Acids Res. 48, 2694-2708. (10.1093/nar/gkz1215) PubMed DOI PMC

Berriman M, et al. 2005. The genome of the African trypanosome Trypanosoma brucei. Science 309, 416-422. (10.1126/science.1112642) PubMed DOI

Ivens AC, et al. 2005. The genome of the kinetoplastid parasite, Leishmania major. Science 309, 436-442. (10.1126/science.1112680) PubMed DOI PMC

Flegontov P, et al. 2016. Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of Leishmania. Sci. Rep. 6, 23704. (10.1038/srep23704) PubMed DOI PMC

Ebenezer TE, et al. 2019. Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biol. 17, 11. (10.1186/s12915-019-0626-8) PubMed DOI PMC

Sevova ES, Bangs JD. 2009. Streamlined architecture and glycosylphosphatidylinositol-dependent trafficking in the early secretory pathway of African trypanosomes. Mol. Biol. Cell 20, 4739-4750. (10.1091/mbc.E09-07-0542) PubMed DOI PMC

Kruzel EK, Zimmett GP, Bangs JD. 2017. Life stage-specific cargo receptors facilitate glycosylphosphatidylinositol-anchored surface coat protein transport in Trypanosoma brucei. mSphere 2, e00282-17. (10.1128/msphere.00282-17) PubMed DOI PMC

Demmel L, Melak M, Kotisch H, Fendos J, Reipert S, Warren G. 2011. Differential selection of golgi proteins by COPII Sec24 isoforms in procyclic Trypanosoma brucei. Traffic 12, 1575-1591. (10.1111/j.1600-0854.2011.01257.x) PubMed DOI

Obado SO, Brillantes M, Uryu K, Zhang W, Ketaren NE, Chait BT, Field MC, Rout MP. 2016. Interactome mapping reveals the evolutionary history of the nuclear pore complex. PLoS Biol. 14, e1002365. (10.1371/journal.pbio.1002365) PubMed DOI PMC

Roger AJ, Susko E, Leger MM. 2021. Evolution: Reconstructing the timeline of eukaryogenesis. Curr. Biol. 31, R193-R196. (10.1016/j.cub.2020.12.035) PubMed DOI

Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. 2017. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711-723. (10.1038/nrmicro.2017.133) PubMed DOI

Koonin EV. 2015. Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? Phil. Trans. R. Soc. B 370, 20140333. (10.1098/rstb.2014.0333) PubMed DOI PMC

Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, Sali A, Rout MP. 2004. Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2, e380. (10.1371/journal.pbio.0020380) PubMed DOI PMC

DeGrasse JA, Dubois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT. 2009. Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Mol. Cell. Proteomics 8, 2119-2130. (10.1074/mcp.M900038-MCP200) PubMed DOI PMC

Sevova ES, Bangs JD. 2009. Streamlined architecture and glycosylphosphatidylinositol-dependent trafficking in the early secretory pathway of African trypanosomes. Mol. Biol. Cell. 20, 4739-4750. (10.1091/mbc.e09-07-0542) PubMed DOI PMC

Wang YN, Wang M, Field MC. 2010. Trypanosoma brucei: Trypanosome-specific endoplasmic reticulum proteins involved in variant surface glycoprotein expression. Exp. Parasitol. 125, 208-221. (10.1016/j.exppara.2010.01.015) PubMed DOI PMC

Hu H, Gourguechon S, Wang CC, Li Z. 2016. The G1 cyclin-dependent kinase CRK1 in Trypanosoma brucei regulates anterograde protein transport by phosphorylating the COPII subunit Sec31. J. Biol. Chem. 291, 15 527-15 539. (10.1074/jbc.M116.715185) PubMed DOI PMC

Sealey-Cardona M, Schmidt K, Demmel L, Hirschmugl T, Gesell T, Dong G, Warren G. 2014. Sec16 determines the size and functioning of the Golgi in the protist parasite, Trypanosoma brucei. Traffic 15, 613-629. (10.1111/tra.12170) PubMed DOI

Tashyreva D, et al. 2018. Phylogeny and morphology of new diplonemids from Japan. Protist 169, 158-179. (10.1016/j.protis.2018.02.001) PubMed DOI

Prokopchuk G, Tashyreva D, Yabuki A, Horák A, Masařová P, Lukeš J. 2019. Morphological, ultrastructural, motility and evolutionary characterization of two new Hemistasiidae species. Protist 170, 259-282. (10.1016/j.protis.2019.04.001) PubMed DOI

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410. (10.1016/S0022-2836(05)80360-2) PubMed DOI

Jackson AP, et al. 2016. Kinetoplastid phylogenomics reveals the evolutionary innovations associated with the origins of parasitism. Curr. Biol. 26, 161-172. (10.1016/j.cub.2015.11.055) PubMed DOI PMC

Záhonová K, et al. 2018. Peculiar features of the plastids of the colourless alga Euglena longa and photosynthetic euglenophytes unveiled by transcriptome analyses. Sci. Rep. 8, 17012. (10.1038/s41598-018-35389-1) PubMed DOI PMC

Keeling PJ, et al. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 12, e1001889. (10.1371/journal.pbio.1001889) PubMed DOI PMC

Johnson LK, Alexander H, Brown CT. 2017. (all datasets) MMETSP re-assemblies [Data set]. Zenodo. (10.5281/zenodo.257410) DOI

Eddy SR. 2009. A new generation of homology search tools based on probabilistic inference. Genome Inf. 23, 205-211. (10.1142/9781848165632_0019) PubMed DOI

Jones P, et al. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236-1240. (10.1093/bioinformatics/btu031) PubMed DOI PMC

Kearse M, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649. (10.1093/bioinformatics/bts199) PubMed DOI PMC

Jumper J, et al. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583-589. (10.1038/s41586-021-03819-2) PubMed DOI PMC

Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. 2021. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 30, 70-82. (10.1002/pro.3943) PubMed DOI PMC

Remmert M, Biegert A, Hauser A, Söding J. 2012. HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9, 173-175. (10.1038/nmeth.1818) PubMed DOI

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780. (10.1093/molbev/mst010) PubMed DOI PMC

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973. (10.1093/bioinformatics/btp348) PubMed DOI PMC

Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313. (10.1093/bioinformatics/btu033) PubMed DOI PMC

Ronquist F, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61, 539-542. (10.1093/sysbio/sys029) PubMed DOI PMC

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Von Haeseler A, Lanfear R, Teeling E. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530-1534. (10.1093/molbev/msaa015) PubMed DOI PMC

Kaur B, Valach M, Peña-Diaz P, Moreira S, Keeling PJ, Burger G, Lukeš J, Faktorová D. 2018. Transformation of Diplonema papillatum, the type species of the highly diverse and abundant marine microeukaryotes Diplonemida (Euglenozoa). Environ. Microbiol. 20, 1030-1040. (10.1111/1462-2920.14041) PubMed DOI

Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. 2011. Andromeda: A peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805. (10.1021/pr101065j) PubMed DOI

Zoltner M, et al. 2020. Suramin exposure alters cellular metabolism and mitochondrial energy production in African trypanosomes. J. Biol. Chem. 295, 8331-8347. (10.1074/jbc.RA120.012355) PubMed DOI PMC

Yurchenko V, Votỳpka J, Tesařová M, Klepetková H, Kraeva N, Jirku M, Lukeš J. 2014. Ultrastructure and molecular phylogeny of four new species of monoxenous trypanosomatids from flies (Diptera: Brachycera) with redefinition of the genus Wallaceina. Folia Parasitol. 61, 97-112. (10.14411/fp.2014.023) PubMed DOI

Perez-Riverol Y, et al. 2022. The PRIDE database resources in 2022: A hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543-D552. (10.1093/nar/gkab1038) PubMed DOI PMC

Faktorová D, Záhonová K, Benz C, Dacks JB, Field MC, Lukeš J. 2023. Functional differentiation of Sec13 paralogues in the euglenozoan protists. Figshare. (10.6084/m9.figshare.c.6673618) PubMed DOI PMC

On the possibility of yet a third kinetochore system in the protist phylum Euglenozoa

Ultrastructure and 3D reconstruction of a diplonemid protist (Diplonemea) and its novel membranous organelle

Functional differentiation of Sec13 paralogues in the euglenozoan protists

Zobrazit více v PubMed

figshare
10.6084/m9.figshare.c.6673618