Determining the targeting specificity of the selective peroxisomal targeting factor Pex9.
Saccharomyces cerevisiae
PTS1
Pex5
Pex9
peroxisome
protein targeting
Journal
Biological chemistry
ISSN: 1437-4315
Titre abrégé: Biol Chem
Pays: Germany
ID NLM: 9700112
Informations de publication
Date de publication:
23 02 2023
23 02 2023
Historique:
received:
06
02
2022
accepted:
24
08
2022
pubmed:
25
10
2022
medline:
17
2
2023
entrez:
24
10
2022
Statut:
epublish
Résumé
Accurate and regulated protein targeting is crucial for cellular function and proteostasis. In the yeast
Identifiants
pubmed: 36279206
pii: hsz-2022-0116
doi: 10.1515/hsz-2022-0116
doi:
Substances chimiques
Peroxisome-Targeting Signal 1 Receptor
0
Saccharomyces cerevisiae Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
121-133Informations de copyright
© 2022 the author(s), published by De Gruyter, Berlin/Boston.
Références
Aviram, N. and Schuldiner, M. (2017). Targeting and translocation of proteins to the endoplasmic reticulum at a glance. J. Cell Sci. 130: 4079–4085, https://doi.org/10.1242/jcs.204396 .
doi: 10.1242/jcs.204396
Barreto, L., Garcerá, A., Jansson, K., Sunnerhagen, P., and Herrero, E. (2006). A peroxisomal glutathione transferase of Saccharomyces cerevisiae is functionally related to sulfur amino acid metabolism. Eukaryot. Cell 5: 1748–1759, https://doi.org/10.1128/ec.00216-06 .
doi: 10.1128/ec.00216-06
Brachmann, C.B., Davies, A., Cost, G.J., Caputo, E., Li, J., Hieter, P., and Boeke, J.D. (1998). Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115–132, https://doi.org/10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2 .
Brocard, C. and Hartig, A. (2006). Peroxisome targeting signal 1: is it really a simple tripeptide? Biochim. Biophys. Acta. Mol. Cell Res. 1763: 1565–1573, https://doi.org/10.1016/j.bbamcr.2006.08.022 .
doi: 10.1016/j.bbamcr.2006.08.022
Chevray, P.M. and Nathans, D. (1992). Protein interaction cloning in yeast: identification of mammalian proteins that react with the leucine zipper of Jun. Proc. Natl. Acad. Sci. U.S.A. 89: 5789–5793, https://doi.org/10.1073/pnas.89.13.5789 .
doi: 10.1073/pnas.89.13.5789
Cohen, Y. and Schuldiner, M. (2011). Advanced methods for high-throughput microscopy screening of genetically modified yeast libraries. Methods Mol. Biol. 781: 127–159, https://doi.org/10.1007/978-1-61779-276-2_8 .
doi: 10.1007/978-1-61779-276-2_8
Daniel Gietz, R. and Woods, R.A. (2002). Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. In: Guthrie, C. and Fink, G.R. (Eds.), Guide to yeast genetics and molecular and cell biology - Part B . Academic Press, p. 87–96.
DeLoache, W.C., Russ, Z.N., and Dueber, J.E. (2016). Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nat. Commun. 7: 11152, https://doi.org/10.1038/ncomms11152 .
doi: 10.1038/ncomms11152
Effelsberg, D., Cruz-Zaragoza, L.D., Tonillo, J., Schliebs, W., and Erdmann, R. (2015). Role of Pex21p for piggyback import of Gpd1p and Pnc1p into peroxisomes of Saccharomyces cerevisiae. J. Biol. Chem. 290: 25333–25342, https://doi.org/10.1074/jbc.m115.653451 .
doi: 10.1074/jbc.m115.653451
Effelsberg, D., Cruz-Zaragoza, L.D., Schliebs, W., and Erdmann, R. (2016). Pex9p is a new yeast peroxisomal import receptor for PTS1-containing proteins. J. Cell Sci. 129: 4057–4066, https://doi.org/10.1242/jcs.195271 .
doi: 10.1242/jcs.195271
Fodor, K., Wolf, J., Erdmann, R., Schliebs, W., and Wilmanns, M. (2012). Molecular requirements for peroxisomal targeting of alanine-glyoxylate aminotransferase as an essential determinant in primary hyperoxaluria type 1. Plos Biol. 10: e1001309, https://doi.org/10.1371/journal.pbio.1001309 .
doi: 10.1371/journal.pbio.1001309
Gabay-Maskit, S., Cruz-Zaragoza, L.D., Shai, N., Eisenstein, M., Bibi, C., Cohen, N., Hansen, T., Yifrach, E., Harpaz, N., Belostotsky, R., et al.. (2020). A piggybacking mechanism enables peroxisomal localization of the glyoxylate cycle enzyme Mdh2 in yeast. J. Cell Sci. 133: 244376, https://doi.org/10.1242/jcs.244376 .
doi: 10.1242/jcs.244376
Gatto, G.J., Geisbrecht, B.V., Gould, S.J., and Berg, J.M. (2000). Peroxisomal targeting signal-1 recognition by the TPR domains of human PEX5. Nat. Struct. Biol. 7: 1091–1095, https://doi.org/10.1038/81930 .
doi: 10.1038/81930
Gerondopoulos, A., Bräuer, P., Sobajima, T., Wu, Z., Parker, J.L., Biggin, P.C., Barr, F.A., and Newstead, S. (2021). A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrieval. Elife 10, https://doi.org/10.7554/eLife.68380 .
doi: 10.7554/eLife.68380
Hagen, S., Drepper, F., Fischer, S., Fodor, K., Passon, D., Platta, H.W., Zenn, M., Schliebs, W., Girzalsky, W., Wilmanns, M., et al.. (2015). Structural insights into cargo recognition by the yeast PTS1 receptor. J. Biol. Chem. 290: 26610–26626, https://doi.org/10.1074/jbc.m115.657973 .
doi: 10.1074/jbc.m115.657973
Hanscho, M., Ruckerbauer, D.E., Chauhan, N., Hofbauer, H.F., Krahulec, S., Nidetzky, B., Kohlwein, S.D., Zanghellini, J., and Natter, K. (2012). Nutritional requirements of the BY series of Saccharomyces cerevisiae strains for optimum growth. FEMS Yeast Res. 12: 796–808, https://doi.org/10.1111/j.1567-1364.2012.00830.x .
doi: 10.1111/j.1567-1364.2012.00830.x
Hegde, R.S. and Zavodszky, E. (2019). Recognition and degradation of mislocalized proteins in health and disease. Cold Spring Harbor. Perspect. Biol. 11: a033902, https://doi.org/10.1101/cshperspect.a033902 .
doi: 10.1101/cshperspect.a033902
Hochreiter, B., Chong, C.-S., Hartig, A., Maurer-Stroh, S., Berger, J., Schmid, J.A., and Kunze, M. (2020). A novel FRET approach quantifies the interaction strength of peroxisomal targeting signals and their receptor in living cells. Cells 9: 2381, https://doi.org/10.3390/cells9112381 .
doi: 10.3390/cells9112381
Islinger, M., Voelkl, A., Fahimi, H.D., and Schrader, M. (2018). The peroxisome: an update on mysteries 2.0. Histochem. Cell Biol. 150: 443–471, https://doi.org/10.1007/s00418-018-1722-5 .
doi: 10.1007/s00418-018-1722-5
James, P., Halladay, J., and Craig, E.A. (1996). Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144: 1425–1436, https://doi.org/10.1093/genetics/144.4.1425 .
doi: 10.1093/genetics/144.4.1425
Janke, C., Magiera, M.M., Rathfelder, N., Taxis, C., Reber, S., Maekawa, H., Moreno-Borchart, A., Doenges, G., Schwob, E., Schiebel, E., et al.. (2004). A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21: 947–962, https://doi.org/10.1002/yea.1142 .
doi: 10.1002/yea.1142
Kerssen, D., Hambruch, E., Klaas, W., Platta, H.W., de Kruijff, B., Erdmann, R., Kunau, W.-H., and Schliebs, W. (2006). Membrane association of the cycling peroxisome import receptor Pex5p. J. Biol. Chem. 281: 27003–27015, https://doi.org/10.1074/jbc.m509257200 .
doi: 10.1074/jbc.m509257200
Konopka, J.B. (1993). AFR1 acts in conjunction with the alpha-factor receptor to promote morphogenesis and adaptation. Mol. Cell Biol. 13: 6876–6888, https://doi.org/10.1128/mcb.13.11.6876-6888.1993 .
doi: 10.1128/mcb.13.11.6876-6888.1993
Kunze, M., Kragler, F., Binder, M., Hartig, A., and Gurvitz, A. (2002). Targeting of malate synthase 1 to the peroxisomes of Saccharomyces cerevisiae cells depends on growth on oleic acid medium. Eur. J. Biochem. 269: 915–922, https://doi.org/10.1046/j.0014-2956.2001.02727.x .
doi: 10.1046/j.0014-2956.2001.02727.x
Lametschwandtner, G., Brocard, C., Fransen, M., Van Veldhoven, P., Berger, J., and Hartig, A. (1998). The difference in recognition of terminal tripeptides as peroxisomal targeting signal 1 between yeast and human is due to different affinities of their receptor Pex5p to the cognate signal and to residues adjacent to it. J. Biol. Chem. 273: 33635–33643, https://doi.org/10.1074/jbc.273.50.33635 .
doi: 10.1074/jbc.273.50.33635
Laurila, K. and Vihinen, M. (2009). Prediction of disease-related mutations affecting protein localization. BMC Genom. 10: 122, https://doi.org/10.1186/1471-2164-10-122 .
doi: 10.1186/1471-2164-10-122
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25: 1605–1612, https://doi.org/10.1002/jcc.20084 .
doi: 10.1002/jcc.20084
Rosenthal, M., Metzl-Raz, E., Bürgi, J., Yifrach, E., Drwesh, L., Fadel, A., Peleg, Y., Rapaport, D., Wilmanns, M., Barkai, N., et al.. (2020). Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay. Proc. Natl. Acad. Sci. U.S.A. 117: 201920078, https://doi.org/10.1073/pnas.1920078117 .
doi: 10.1073/pnas.1920078117
Šali, A. and Blundell, T.L. (1993). Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779–815.
Schaeffer, C., Creatore, A., and Rampoldi, L. (2014). Protein trafficking defects in inherited kidney diseases. Nephrol. Dial. Transplant. 29: iv33–iv44, https://doi.org/10.1093/ndt/gfu231 .
doi: 10.1093/ndt/gfu231
Schreiber, G. and Keating, A.E. (2011). Protein binding specificity versus promiscuity. Curr. Opin. Struct. Biol. 21: 50–61, https://doi.org/10.1016/j.sbi.2010.10.002 .
doi: 10.1016/j.sbi.2010.10.002
Stanley, W.A., Filipp, F.V., Kursula, P., Schüller, N., Erdmann, R., Schliebs, W., Sattler, M., and Wilmanns, M. (2006). Recognition of a functional peroxisome type 1 target by the dynamic import receptor Pex5p. Mol. Cell 24: 653–663, https://doi.org/10.1016/j.molcel.2006.10.024 .
doi: 10.1016/j.molcel.2006.10.024
Tong, A.H. and Boone, C. (2006). Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol. Biol. 313: 171–192, https://doi.org/10.1385/1-59259-958-3:171 .
Trinquier, G. and Sanejouand, Y.H. (1998). Which effective property of amino acids is best preserved by the genetic code? Protein Eng. 11: 153–169, https://doi.org/10.1093/protein/11.3.153 .
doi: 10.1093/protein/11.3.153
Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E., and Berendsen, H.J.C. (2005). GROMACS: fast, flexible, and free. J. Comput. Chem. 26: 1701–1718, https://doi.org/10.1002/jcc.20291 .
doi: 10.1002/jcc.20291
Walter, T. and Erdmann, R. (2019). Current advances in protein import into peroxisomes. Protein J. 38: 351–362, https://doi.org/10.1007/s10930-019-09835-6 .
doi: 10.1007/s10930-019-09835-6
Weill, U., Yofe, I., Sass, E., Stynen, B., Davidi, D., Natarajan, J., Ben-Menachem, R., Avihou, Z., Goldman, O., Harpaz, N., et al.. (2018). Genome-wide SWAp-Tag yeast libraries for proteome exploration. Nat. Methods 15: 617–622, https://doi.org/10.1038/s41592-018-0044-9 .
doi: 10.1038/s41592-018-0044-9
Yifrach, E., Chuartzman, S.G., Dahan, N., Maskit, S., Zada, L., Weill, U., Yofe, I., Olender, T., Schuldiner, M., and Zalckvar, E. (2016). Characterization of proteome dynamics during growth in oleate reveals a new peroxisome-targeting receptor. J. Cell Sci. 129: 4067–4075, https://doi.org/10.1242/jcs.195255 .
doi: 10.1242/jcs.195255
Yifrach, E., Holbrook-Smith, D., Bürgi, J., Othman, A., Eisenstein, M., Van Roermund, C.W.T., Visser, W., Tirosh, A., Bibi, C., Galor, S., et al.. (2021). Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions . bioRxiv, Rehovot.
Yofe, I. and Schuldiner, M. (2014). Primers-4-Yeast: a comprehensive web tool for planning primers for Saccharomyces cerevisiae. Yeast 31: 77–80, https://doi.org/10.1002/yea.2998 .
doi: 10.1002/yea.2998
Yofe, I., Weill, U., Meurer, M., Chuartzman, S., Zalckvar, E., Goldman, O., Ben-Dor, S., Schutze, C., Wiedemann, N., Knop, M., et al.. (2016). One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat. Methods 13: 371–378, https://doi.org/10.1038/nmeth.3795 .
doi: 10.1038/nmeth.3795