Einzeltreffer — DigiBib

Peroxisomes are organelles that carry out β-oxidation of fatty acids and amino acids. Both rare and prevalent diseases are caused by their dysfunction 1 . Among disease-causing variant genes are those required for protein transport into peroxisomes. The peroxisomal protein import machinery, which also shares similarities with chloroplasts 2 , is unique in transporting folded and large, up to 10 nm in diameter, protein complexes into peroxisomes 3 . Current models postulate a large pore formed by transmembrane proteins 4 ; however, so far, no pore structure has been observed. In the budding yeast Saccharomyces cerevisiae, the minimum transport machinery includes the membrane proteins Pex13 and Pex14 and the cargo-protein-binding transport receptor, Pex5. Here we show that Pex13 undergoes liquid-liquid phase separation (LLPS) with Pex5-cargo. Intrinsically disordered regions in Pex13 and Pex5 resemble those found in nuclear pore complex proteins. Peroxisomal protein import depends on both the number and pattern of aromatic residues in these intrinsically disordered regions, consistent with their roles as 'stickers' in associative polymer models of LLPS 5,6 . Finally, imaging fluorescence cross-correlation spectroscopy shows that cargo import correlates with transient focusing of GFP-Pex13 and GFP-Pex14 on the peroxisome membrane. Pex13 and Pex14 form foci in distinct time frames, suggesting that they may form channels at different saturating concentrations of Pex5-cargo. Our findings lead us to suggest a model in which LLPS of Pex5-cargo with Pex13 and Pex14 results in transient protein transport channels 7 .

Titel:	Peroxisome biogenesis initiated by protein phase separation.
Autor/in / Beteiligte Person:	Ravindran, R ; Bacellar, IOL ; Castellanos-Girouard, X ; Wahba, HM ; Zhang, Z ; Omichinski, JG ; Kisley, L ; Michnick, SW
Zeitschrift:	Nature, Jg. 617 (2023-05-01), Heft 7961, S. 608-615
Veröffentlichung:	Basingstoke : Nature Publishing Group ; <i>Original Publication</i>: London, Macmillan Journals ltd., 2023
Medientyp:	academicJournal
ISSN:	1476-4687 (electronic)
DOI:	10.1038/s41586-023-06044-1
Schlagwort:	Intracellular Membranes chemistry Intracellular Membranes metabolism Peroxisome-Targeting Signal 1 Receptor chemistry Peroxisome-Targeting Signal 1 Receptor metabolism Phase Transition Protein Binding Protein Transport Intrinsically Disordered Proteins chemistry Intrinsically Disordered Proteins metabolism Membrane Proteins chemistry Membrane Proteins metabolism Peroxins chemistry Peroxins metabolism Peroxisomes chemistry Peroxisomes metabolism Saccharomyces cerevisiae chemistry Saccharomyces cerevisiae cytology Saccharomyces cerevisiae metabolism Saccharomyces cerevisiae Proteins chemistry Saccharomyces cerevisiae Proteins metabolism
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article Language: English [Nature] 2023 May; Vol. 617 (7961), pp. 608-615. <i>Date of Electronic Publication: </i>2023 May 10. MeSH Terms: Membrane Proteins* / chemistry ; Membrane Proteins* / metabolism ; Peroxins* / chemistry ; Peroxins* / metabolism ; Peroxisomes* / chemistry ; Peroxisomes* / metabolism ; Saccharomyces cerevisiae* / chemistry ; Saccharomyces cerevisiae* / cytology ; Saccharomyces cerevisiae* / metabolism ; Saccharomyces cerevisiae Proteins* / chemistry ; Saccharomyces cerevisiae Proteins* / metabolism ; Intracellular Membranes / chemistry ; Intracellular Membranes / metabolism ; Peroxisome-Targeting Signal 1 Receptor / chemistry ; Peroxisome-Targeting Signal 1 Receptor / metabolism ; Phase Transition ; Protein Binding ; Protein Transport ; Intrinsically Disordered Proteins / chemistry ; Intrinsically Disordered Proteins / metabolism References: Zalckvar, E. & Schuldiner, M. Beyond rare disorders: a new era for peroxisomal pathophysiology. Mol. Cell 82, 2228–2235 (2022). (PMID: 3571458410.1016/j.molcel.2022.05.028) ; Ganesan, I., Shi, L. X., Labs, M. & Theg, S. M. Evaluating the functional pore size of chloroplast TOC and TIC protein translocons: import of folded proteins. Plant Cell 30, 2161–2173 (2018). (PMID: 30104404618102110.1105/tpc.18.00427) ; Walton, P. A., Hill, P. E. & Subramani, S. Import of stably folded proteins into peroxisomes. Mol. Biol. Cell 6, 675–683 (1995). (PMID: 757968730122810.1091/mbc.6.6.675) ; Meinecke, M. et al. The peroxisomal importomer constitutes a large and highly dynamic pore. Nat. Cell Biol. 12, 273–277 (2010). (PMID: 2015468110.1038/ncb2027) ; Martin, E. W. et al. Valence and patterning of aromatic residues determine the phase behavior of prion-like domains. Science 367, 694–699 (2020). (PMID: 32029630729718710.1126/science.aaw8653) ; Wang, J. et al. A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174, 688–699 (2018). (PMID: 29961577606376010.1016/j.cell.2018.06.006) ; Erdmann, R. & Schliebs, W. Peroxisomal matrix protein import: the transient pore model. Nat. Rev. Mol. Cell Biol. 6, 738–742 (2005). (PMID: 1610387210.1038/nrm1710) ; Gatto, G. J. Jr, Geisbrecht, B. V., Gould, S. J. & Berg, J. M. Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Nat. Struct. Biol. 7, 1091–1095 (2000). (PMID: 1110188710.1038/81930) ; Elgersma, Y. et al. The SH3 domain of the Saccharomyces cerevisiae peroxisomal membrane protein Pex13p functions as a docking site for Pex5p, a mobile receptor for the import PTS1-containing proteins. J. Cell Biol. 135, 97–109 (1996). (PMID: 885816610.1083/jcb.135.1.97) ; Erdmann, R. & Blobel, G. Identification of Pex13p a peroxisomal membrane receptor for the PTS1 recognition factor. J. Cell Biol. 135, 111–121 (1996). (PMID: 885816710.1083/jcb.135.1.111) ; Albertini, M. et al. Pex14p, a peroxisomal membrane protein binding both receptors of the two PTS-dependent import pathways. Cell 89, 83–92 (1997). (PMID: 909471710.1016/S0092-8674(00)80185-3) ; Brocard, C., Lametschwandtner, G., Koudelka, R. & Hartig, A. Pex14p is a member of the protein linkage map of Pex5p. EMBO J. 16, 5491–5500 (1997). (PMID: 9312008117018110.1093/emboj/16.18.5491) ; Francisco, T. et al. Protein transport into peroxisomes: knowns and unknowns. Bioessays https://doi.org/10.1002/bies.201700047 (2017). ; Frey, S., Richter, R. P. & Görlich, D. FG-rich repeats of nuclear pore proteins form a three-dimensional meshwork with hydrogel-like properties. Science 314, 815–817 (2006). (PMID: 1708245610.1126/science.1132516) ; Celetti, G. et al. The liquid state of FG-nucleoporins mimics permeability barrier properties of nuclear pore complexes. J. Cell Biol. https://doi.org/10.1083/jcb.201907157 (2020). ; Paci, G., Caria, J. & Lemke, E. A. Cargo transport through the nuclear pore complex at a glance. J. Cell Sci. 134, jcs247874 (2021). (PMID: 3349535710.1242/jcs.247874) ; Barros-Barbosa, A. et al. The intrinsically disordered nature of the peroxisomal protein translocation machinery. FEBS J. 286, 24–38 (2019). (PMID: 3044398610.1111/febs.14704) ; Emmanouilidis, L., Gopalswamy, M., Passon, D. M., Wilmanns, M. & Sattler, M. Structural biology of the import pathways of peroxisomal matrix proteins. Biochim. Biophys. Acta 1863, 804–813 (2016). (PMID: 2645016610.1016/j.bbamcr.2015.09.034) ; Gould, S. J. & Collins, C. S. Opinion: peroxisomal-protein import: is it really that complex. Nat. Rev. Mol. Cell Biol. 3, 382–389 (2002). (PMID: 1198877210.1038/nrm807) ; Carvalho, A. F. et al. The N-terminal half of the peroxisomal cycling receptor Pex5p is a natively unfolded domain. J. Mol. Biol. 356, 864–875 (2006). (PMID: 1640351710.1016/j.jmb.2005.12.002) ; Lancaster, A. K., Nutter-Upham, A., Lindquist, S. & King, O. D. PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition. Bioinformatics 30, 2501–2502 (2014). (PMID: 24825614414788310.1093/bioinformatics/btu310) ; Hoepfner, D., van den Berg, M., Philippsen, P., Tabak, H. F. & Hettema, E. H. A role for Vps1p, actin, and the Myo2p motor in peroxisome abundance and inheritance in Saccharomyces cerevisiae. J. Cell Biol. 155, 979–990 (2001). (PMID: 11733545215091510.1083/jcb.200107028) ; Yofe, I. et al. Pex35 is a regulator of peroxisome abundance. J. Cell Sci. 130, 791–804 (2017). (PMID: 28049721) ; DeLoache, W. C., Russ, Z. N. & Dueber, J. E. Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nat. Commun. 7, 11152 (2016). (PMID: 27025684547682510.1038/ncomms11152) ; Bremer, A. et al. Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains. Nat. Chem. 14, 196–207 (2022). (PMID: 3493104610.1038/s41557-021-00840-w) ; Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003). (PMID: 1456209510.1038/nature02026) ; Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935–949 (2014). (PMID: 24529477413993710.1016/j.cell.2014.02.001) ; Bergeron-Sandoval, L. P. et al. Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.2113789118 (2021). ; Cooper, J. T. & Harris, J. M. Imaging fluorescence-correlation spectroscopy for measuring fast surface diffusion at liquid/solid interfaces. Anal. Chem. 86, 7618–7626 (2014). (PMID: 2497516910.1021/ac5014354) ; Singh, A. P. & Wohland, T. Applications of imaging fluorescence correlation spectroscopy. Curr. Opin. Chem. Biol. 20, 29–35 (2014). (PMID: 2481415310.1016/j.cbpa.2014.04.006) ; Shuang, B., Chen, J., Kisley, L. & Landes, C. F. Troika of single particle tracking programing: SNR enhancement, particle identification, and mapping. Phys. Chem. Chem. Phys. 16, 624–634 (2014). (PMID: 24263676404158010.1039/C3CP53968G) ; Slaughter, B. D., Schwartz, J. W. & Li, R. Mapping dynamic protein interactions in MAP kinase signaling using live-cell fluorescence fluctuation spectroscopy and imaging. Proc. Natl Acad. Sci. USA 104, 20320–20325 (2007). (PMID: 18077328215442910.1073/pnas.0710336105) ; Cherry, J. M. et al. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 40, D700–705 (2012). (PMID: 2211003710.1093/nar/gkr1029) ; Bacia, K., Kim, S. A. & Schwille, P. Fluorescence cross-correlation spectroscopy in living cells. Nat. Methods 3, 83–89 (2006). (PMID: 1643251610.1038/nmeth822) ; Kisley, L. et al. Characterization of porous materials by fluorescence correlation spectroscopy super-resolution optical fluctuation imaging. ACS Nano 9, 9158–9166 (2015). (PMID: 2623512710.1021/acsnano.5b03430) ; Ouyang, M. et al. Liquid-liquid phase transition drives intra-chloroplast cargo sorting. Cell 180, 1144–1159 (2020). (PMID: 3216921710.1016/j.cell.2020.02.045) ; Gould, S. J. et al. Pex13p is an SH3 protein of the peroxisome membrane and a docking factor for the predominantly cytoplasmic PTs1 receptor. J. Cell Biol. 135, 85–95 (1996). (PMID: 885816510.1083/jcb.135.1.85) ; Girzalsky, W. et al. Involvement of Pex13p in Pex14p localization and peroxisomal targeting signal 2-dependent protein import into peroxisomes. J. Cell Biol. 144, 1151–1162 (1999). (PMID: 10087260215058310.1083/jcb.144.6.1151) ; Kerssen, D. et al. Membrane association of the cycling peroxisome import receptor Pex5p. J. Biol. Chem. 281, 27003–27015 (2006). (PMID: 1684933710.1074/jbc.M509257200) ; Banjade, S. & Rosen, M. K. Phase transitions of multivalent proteins can promote clustering of membrane receptors. Elife 3, e04123 (2014). (PMID: 25321392423805810.7554/eLife.04123) ; Gaussmann, S. et al. Membrane interactions of the peroxisomal proteins PEX5 and PEX14. Front. Cell Dev. Biol. 9, 651449 (2021). (PMID: 33937250808655810.3389/fcell.2021.651449) ; Feng, P. et al. A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel. Nature 607, 374–380 (2022). (PMID: 35768507927915610.1038/s41586-022-04903-x) ; Pedrosa, A. G. et al. Peroxisomal monoubiquitinated PEX5 interacts with the AAA ATPases PEX1 and PEX6 and is unfolded during its dislocation into the cytosol. J. Biol. Chem. 293, 11553–11563 (2018). (PMID: 29884772606519710.1074/jbc.RA118.003669) ; Gao, Y., Skowyra, M. L., Feng, P. & Rapoport, T. A. Protein import into peroxisomes occurs through a nuclear pore-like phase. Science 378, eadf3971 (2022). (PMID: 36520918979557710.1126/science.adf3971) ; Lazard, M., Blanquet, S., Fisicaro, P., Labarraque, G. & Plateau, P. Uptake of selenite by Saccharomyces cerevisiae involves the high and low affinity orthophosphate transporters. J. Biol. Chem. 285, 32029–32037 (2010). (PMID: 20688911295220410.1074/jbc.M110.139865) ; Felice, M. R. et al. Post-transcriptional regulation of the yeast high affinity iron transport system. J. Biol. Chem. 280, 22181–22190 (2005). (PMID: 1581748810.1074/jbc.M414663200) ; Salomons, F. A., Kiel, J. A., Faber, K. N., Veenhuis, M. & van der Klei, I. J. Overproduction of Pex5p stimulates import of alcohol oxidase and dihydroxyacetone synthase in a Hansenula polymorpha Pex14 null mutant. J. Biol. Chem. 275, 12603–12611 (2000). (PMID: 1077755110.1074/jbc.275.17.12603) ; Steinberg, S. et al. The PEX Gene Screen: molecular diagnosis of peroxisome biogenesis disorders in the Zellweger syndrome spectrum. Mol. Genet. Metab. 83, 252–263 (2004). (PMID: 1554239710.1016/j.ymgme.2004.08.008) ; Ebberink, M. S. et al. Genetic classification and mutational spectrum of more than 600 patients with a Zellweger syndrome spectrum disorder. Hum. Mutat. 32, 59–69 (2011). (PMID: 2103159610.1002/humu.21388) ; Jansen, R. L. M., Santana-Molina, C., van den Noort, M., Devos, D. P. & van der Klei, I. J. Comparative genomics of peroxisome biogenesis proteins: making sense of the PEX proteins. Front. Cell Dev. Biol. 9, 654163 (2021). (PMID: 34095119817262810.3389/fcell.2021.654163) ; Yofe, I. et al. One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat. Methods 13, 371–378 (2016). (PMID: 26928762486983510.1038/nmeth.3795) ; Sherman, F. Getting started with yeast. Methods Enzymol. 194, 3–21 (1991). (PMID: 200579410.1016/0076-6879(91)94004-V) ; Shaw, W. M. et al. Engineering a model cell for rational tuning of GPCR signaling. Cell 177, 782–796 (2019). (PMID: 30955892647627310.1016/j.cell.2019.02.023) ; Davis, N. G., Horecka, J. L. & Sprague, G. F. Jr. Cis- and trans-acting functions required for endocytosis of the yeast pheromone receptors. J. Cell Biol. 122, 53–65 (1993). (PMID: 839100210.1083/jcb.122.1.53) ; Mascle, X. H. et al. Acetylation of SUMO1 alters interactions with the SIMs of PML and Daxx in a protein-specific manner. Structure 28 157–168 (2020). ; Ceballos, A. V., McDonald, C. J. & Elbaum-Garfinkle, S. Methods and strategies to quantify phase separation of disordered proteins. Methods Enzymol. 611, 31–50 (2018). (PMID: 30471691668884110.1016/bs.mie.2018.09.037) ; Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012). ; Kisley L. PeroxisomeCorrelationMain_LK20221006.m Zenodo https://doi.org/10.5281/zenodo.7702794 (2023). ; Xavier-Castellanos-Girouard. Xavier-Castellanos-Girouard/Peroxisome-biogenesis-initiated-by-protein-phase-separation: Droplet_Fusion v0.1. Zenodo https://doi.org/10.5281/zenodo.7702890 (2023). Grant Information: R35 GM142466 United States GM NIGMS NIH HHS Substance Nomenclature: 0 (Membrane Proteins) ; 0 (Peroxins) ; 0 (Peroxisome-Targeting Signal 1 Receptor) ; 0 (PEX13 protein, S cerevisiae) ; 0 (PEX14 protein, S cerevisiae) ; 0 (PEX5 protein, S cerevisiae) ; 0 (Saccharomyces cerevisiae Proteins) ; 0 (Intrinsically Disordered Proteins) Entry Date(s): Date Created: 20230510 Date Completed: 20230523 Latest Revision: 20231121 Update Code: 20231215 PubMed Central ID: PMC10302873

Klicken Sie ein Format an und speichern Sie dann die Daten oder geben Sie eine Empfänger-Adresse ein und lassen Sie sich per Email zusenden.

BibTeX Citavi, JabRef, u.a.
(Literaturverwaltung)

PDF kein Volltext!
(Merkzettel, Notizen)

RIS Endnote, Citavi u.a.
(Literaturverwaltung)

MODS
(XML zur Weiterverarbeitung)

oder

Wählen Sie das für Sie passende Zitationsformat und kopieren Sie es dann in die Zwischenablage, lassen es sich per Mail zusenden oder speichern es als PDF-Datei.

Gewünschter Zitations-Stil:

oder

Bitte prüfen Sie, ob die Zitation formal korrekt ist, bevor Sie sie in einer Arbeit verwenden. Benutzen Sie gegebenenfalls den "Exportieren"-Dialog, wenn Sie ein Literaturverwaltungsprogramm verwenden und die Zitat-Angaben selbst formatieren wollen.

Peroxisome biogenesis initiated by protein phase separation.