Abstract
This review focuses on events involved in the biogenesis of the lysosome. This organelle contains a diverse array of soluble, luminal proteins capable of digesting all the macromolecules in the cell. Altered function of lysosomes or its constituent enzymes has been implicated in a host of human pathologies, including storage diseases, cancer, and infectious and neurodegenerative diseases. Luminal enzymes are well-characterized, and aspects of how they are incorporated into lysosomes are known. However, little is known about the composition of the membrane surrounding the organelle or how the membrane is assembled. Our starting point to study lysosome biogenesis is to define the composition of the membrane by the use of proven methods for purification of lysosomes to near homogeneity and then to characterize membrane-associated and integral lysosomal membrane proteins. This has been achieved using advanced proteomics (electrophoretic or chromatographic separations of proteins followed by time-of-flight mass spectrometric identification of peptide sequences). To date, we have identified 55 proteins in the membrane-associated fraction and 215 proteins in the integral membrane. By applying these methods to mouse models of lysosome dysgenesis (such as BEIGE, Pale Ear, PEARL) that are related to human diseases such as Chediak-Higashi and Hermansky-Pudlak syndromes, it may be possible to define the membrane protein composition of lysosomes in each of these mutants and to determine how they differ from normal. Identifying proteins affected in the respective mutants may provide hints about how they are targeted to the lysosomal membrane and how failure to target them leads to disease; these features are pivotal to understanding lysosome biogenesis and have the potential to implicate lysosomes in a broad range of human pathologies.
References
Derry D. M., Fawcett J. S., Andermann F., and Wolfe L. S. (1968). Late infantile systemic lipidosis: major monosialogangliosidosis, delineation of two types. Neurology 18, 340–348.
Wolfe L. S., Callahan J., Fawcett J. S., Andermann F., and Scriver C. R. (1970). GM1-gangliosidosis without chrondrodystrophy or visceromegaly. Neurology 20, 23–44.
De Duve C. (1973). In: Lysosomes in Biology and Pathology, Vol. 1, Dingle J. T. and Fell H. B., eds., Amsterdam: North-Holland, pp. 3–40,
Ellgaard L. and Helenius A. (2003). Quality control in the endoplasmic reticulum. Nat. Rev. Molec. Cell Biol. 4, 181–191.
Robinson M. S. (2004). Adaptable adaptors for coated vesicles. Trends Cell Biol. 14, 167–174.
Kornfeld S. and Mellman I. (1989). The biogenesis of lysosomes. Annu. Rev. Cell Biol. 5, 483–525.
Reitman M. L. and Kornfeld S. (1981). Lysosomal enzyme targeting. N-Acetylglucosaminyl-phosphotransferase selectively phosphorylates native lysosomal enzymes. J. Biol. Chem. 256, 11,977–11,980.
Hunziker W. and Geuze H. J. (1996). Intracellular trafficking of lysosomal membrane proteins. BioEssays 18, 379–389.
Reusch U., Bernhard O., Koszinowski U., and Schu P. (2002). AP-1A and AP-3A lysosomal sorting functions. Traffic 3, 752–761.
Eskelinen E. L., Tanaka Y., and Saftig P. (2003). At the acidic edge: emerging functions for lysosomal membrane proteins. Trends Cell Biol. 13, 137–145.
Rodionov D. G., Honing S., Silye A., Kongsvik T. L., Von Figura K., and Bakke O. (2002). Structural requirements for interaction between leucine-sorting signals and clathrin-associated adaptor protein complex AP3. J. Biol. Chem. 277, 47,436–47,443.
Hirst J. and Robinson M. S. (1998). Clathrin and adaptors. Biochim. Biophys. Acta. 1404, 173–193.
Le Borgne R., Alconada A., Bauer U., and Hoflack B. (1998). The mammalian AP-3 adaptor-like complex mediates the intracellular transport of lysosomal membrane glycoproteins. J. Biol. Chem. 273, 29,451–29,461.
Boehm M., and Bonifacino J. S. (2002). Genetic analyses of adaptin function from yeast to mammals. Gene 286, 175–186.
Huizing M. and Gahl W. A. (2002). Disorders of vesicles of lysosomal lineage: the Hermansky-Pudlak syndromes. Curr. Molec. Med. 2, 451–467.
Kornfeld S. (1990). Lysosomal enzyme targeting. Biochem. Soc. Trans. 18, 367–374.
Finbow M. E., and Harrison M. A. (1997). The vacuolar H+-ATPase: a universal proton pump of eukaryotes. Biochem. J. 324, 697–712.
Forgac M. (1996). Regulation of vacuolar acidification. Soc. Gen. Physiol. Series 51, 121–132.
Garin J., Diez R., Kieffer S., et al. (2001). The phagosome proteome: insight into phagosome functions. J Cell Biol 152, 165–180.
Jaiswal J. K., Chakrabarti S., Andrews N. W., and Siimon S. M. (2004). Synaptotagmin VII restricts fusion pore expansion during lysosomal exocytosis. PLoS Biol. 2, 1–9.
Rao S. K., Huynh C., Proux-Gillardeaux V., Galli T., and Andrews N. W. (2004). Identification of SNAREs involved in Synaptotagmin vVII-regulated lysosomal exocytosis. J. Biol. Chem. 279, 20,471–20,479.
Morales C., Clermont Y., and Nadler N. J. (1986). Cyclic endocytic activity and kinetics of lysosomes in Sertoli cells of the rat: a morphometric analysis. Biol. Reprod. 34, 207–218.
Clermont Y., Morales C., and Hermo L. (1987). Endocytic activities of Sertoli cells in the rat. Ann. NY Acad. Sci. 513, 1–15.
Schmid S. L. (1997). Clathrin-coated vesicle formation and protein sorting: an integrated process. Ann. Rev. Biochem. 66, 511–548.
Kirchhausen T. (2000). Clathrin. Ann. Rev. Biochem. 69, 699–727.
Stephens L., Ellson C., and Hawkins P. (2002). Roles of PI3Ks in leukocyte chemotaxis and phagocytosis. Curr. Opin. Cell Biol. 14, 203–213.
Advani R. J., Yang B., Prekeris R., Lee K. C., Klumperman J., and Scheller R. H. (1999). VAMP-7 mediates vesicular transport from endosomes to lysosomes. J. Cell Biol. 146, 765–776.
Klionsky D. J. and Emr S. D. (2000). Autophagy as a regulated pathway of cellular degradation. Science 290, 1717–1721.
Suriapranata I., Epple U. D., Bernreuther D., Bredschneider M., Sovarasteanu K., and Thumm M. (2000). The breakdown of autophagic vesicles inside the vacuole depends on Aut4p. J. Cell Sci. 113, 4025–4033.
Claus V., Jahraus A., Tjelle T., et al. (1998). Lysosomal enzyme trafficking between phagosomes, endosomes, and lysosomes in J774 macrophages. Enrichment of cathepsin H in early endosomes. J. Biol. Chem. 273, 9842–9851.
Kauppi M., Simonsen A., Bremnes B., et al. (2002). The small GTPase Rab22 interacts with EEA1 and controls endosomal membrane trafficking. J. Cell Sci. 115, 899–911.
Callahan J. W. (1999). Molecular basis of GM1 gangliosidosis and Morquio disease, type B. Structure-function studies of lysosomal beta-galactosidase and the non- lysosomal beta-galactosidase-like protein. Biochim. Biophys. Acta. 1455, 85–103.
Mahuran D. J. (1999). Biochemical consequences of mutations causing the GM2 gangliosidoses. Biochim. Biophys. Acta. 1455, 105–138.
Bame K. J. and Rome L. H. (1985). Acetyl coenzyme A: alpha-glucosaminide N-acetyltransferase. Evidence for a transmembrane acetylation mechanism. J. Biol. Chem. 260, 11,293–11,299.
Shih V. E., Axel S. M., Tewksbury J. C., Watkins D., Cooper B. A., and Rosenblatt D. S. (1989). Defective lysosomal release of vitamin B12 (cb1F): A hereditary cobalamin metabolic disorder associated with sudden death. Am. J. Med. Genet. 33, 555–563.
Rosenblatt D. S., Hosack A., Matiaszuk N. V., Cooper B. A., and Laframboise R. (1985). Defect in vitamin B12 release from lysosomes: A newly described inborn error of vitamin B12 metabolism. Science 228, 1319–1321.
Carstea E. D., Morris J. A., Coleman K. G., et al. (1997). Niemann-Pick C1 disease gene: homology to mediators of cholesterol homeostasis. Science 277, 228–231.
Cruz J. C., Sugii S., Yu C., and Chang T. Y. (2000). Role of Niemann-Pick type C1 protein in intracellular trafficking of low density lipoproteinderived cholesterol. J. Biol. Chem. 275, 4013–4021.
Millat G., Marçais C., Tomasetto C., et al. (2001). Niemann-Pick C1 disease: Correlations between NPC1 mutations, levels of NPC1 protein, and phenotypes emphasize the functional significance of the putative sterol-sensing domain and of the cysteine-rich luminal loop. Am. J. Hum. Genet. 68, 1373–1385.
Aula N., Salomaki P., Timonen R., et al. (2000). The spectrum of SLC17A5-gene mutations resulting in free sialic acid-storage diseases indicates some genotype-phenotype correlation. Am. J. Hum. Genet. 67, 832–840.
Gahl W. A. (1987). Disorders of lysosomal membrane transport-cystinosis and Salla disease. Enzyme 38, 154–160.
Kalatzis V., Cherqui S., Antignac C., and Gasnier B. (2001). Cystinosin, the protein defective in cystinosis, is a H+-driven lysosomal cystine transporter. EMBO J. 20, 5940–5949.
Phornphutkul C., Anikster Y., Huizing M., et al. (2001). The promoter of a lysosomal membrane transporter gene, CTNS, binds Sp-1, shares sequences with the promoter of an adjacent gene, carkl, and causes cystinosis if mutated in a critical region. Am. J. Hum. Genet. 69, 712–721.
Pearce D. A. (2000). Localization and processing of CLN3, the protein associated to Batten disease: where is it and what does it do? J. Neurosci. Res. 59, 19–23.
Savukoski M., Klockars T., Holmberg V., Santavuori P., Lander E. S., and Peltonen L. (1998). CLN5, a novel gene encoding a putative transmembrane protein mutated in Finnish variant late infantile neuronal ceroid lipofuscinosis. Nat. Genet. 19, 286–288.
Nishino I., Fu J., Tanji K., et al. (2000). Primary LAMP-2 deficiency causes X-linked vacuolar cardiomyopathy and myopathy (Danon disease). Nature 406, 906–910.
Scimeca J. C., Quincey D., Parrinello H., et al. (2003). Novel mutations in the TCIRG1 gene encoding the a3 subunit of the vacuolar proton pump in patients affected by infantile malignant osteopetrosis. Hum. Mutat. 21, 151–157.
Inaba K., Turley S., Iyoda T., et al. (2000). The formation of immunogenic major histocompatibility complex class II- peptide ligands in lysosomal compartments of dendritic cells is regulated by inflammatory stimuli. J. Exp. Med. 191, 927–936.
Zimmer K. P., Buning J., Weber P., Kaiserlian D., and Strobel S. (2000). Modulation of antigen trafficking to MHC class II-positive late endosomes of enterocytes. Gastroenterology 118, 128–137.
Schroter C. J., Braun M., Englert J., Beck H., Schmid H., and Kalbacher H. (1999). A rapid method to separate endosomes from lysosomal contents using differential centrifugation and hypotonic lysis of lysosomes. J. Immunol. Meth. 227, 161–168.
Künzli B. M., Berberat P. O., Zhu Z. W. W., et al. (2002). Influences of the lysosomal associated membrane proteins (Lamp-1, Lamp-2) and Mac-2 binding protein (Mac-2-BP) on the prognosis of pancreatic carcinoma. Cancer 94, 228–239.
Cabrita M. A., Hobman T. C., Hogue D. L., King K. M., and Cass C. E. (1999). Mouse transporter protein, a membrane protein that regulates cellular multidrug resistance, is localized to lysosomes. Cancer Res. 59, 4890–4897.
Misasi R., Dionisi S., Farilla L., et al. (1997). Gangliosides and autoimmune diabetes. Diabetes Metab. Rev. 13, 163–179.
Ward D. M., Griffiths G. M., Stinchcombe J. C., and Kaplan J. (2000). Analysis of the lysosomal storage disease Chediak-Higashi syndrome. Traffic 1, 816–822.
Huizing M., Anikster Y., and Gahl W. A. (2001). Hermansky-Pudlak syndrome and Chediak-Higashi syndrome: Disorders of vesicle formation and trafficking. Thromb. Haemost. 86, 233–245.
Spritz R. A. (1999). Multi-organellar disorders of pigmentation: intracellular traffic jams in mammals, flies and yeast. Trends Genet. 15, 337–340.
Dell’Angelica E. C., Mullins C., Caplan S., and Bonifacino J. S. (2000). Lysosome-related organelles. FASEB J. 14, 1265–1278.
Perou C. M., Leslie C. M., Green W., Li L., McVey-Ward D., and Kaplan J. (1997). The Beige/Chediak-Higashi syndrome gene encodes a widely expressed cytosolic protein. J. Biol. Chem. 272, 29,790–29,794.
Barbosa M. D., Nguyen Q. A., Tchernev V. T., et al. (1996). Identification of the homologous beige and Chediak-Higashi syndrome genes [published erratum appears in Nature 1997 Jan 2;385(6611):97]. Nature 382, 262–265.
Setaluri V. (2000). Sorting and targeting of melanosomal membrane proteins: signals, pathways, and mechanisms. Pigment Cell Res. 13, 128–134.
Harris E., Wang N., Wu Wl W. L., Weatherford A., De Lozanne A., and Cardelli J. (2002). Dictyostelium LvsB mutants model the lysosomal defects associated with Chediak-Higashi syndrome. Molec. Biol. Cell 13, 656–669.
Huizing M., Scher C. D., Strovel E., et al. (2002). Nonsense mutations in ADTB3A cause complete deficiency of the b3A subunit of adaptor complex-3 and severe Hermansky-Pudlak syndrome type 2. Pediat. Res. 51, 150–158.
Falcon-Perez J. M., Starcevic M., Gautam R., and Dell’Angelica E. C. (2002). BLOC-1, a novel complex containing the Pallidin and Muted proteins in the biogenesis of melanosomes and platelet-dense granules. J. Biol. Chem. 277, 28,191–28,199.
Feng L. J., Novak E. K., Hartnell L. M., Bonifacino J. S., Collinson L. M., and Swank R. T. (2002). The Hermansky-Pudlak syndrome 1 (HPS1) and HPS2 genes independently contribute to the production and function of platelet dense granules, melanosomes, and lysosomes. Blood 99, 1651–1658.
Simmen T., Schmidt A., Hunziker A., and Beermann F. (1999). The tyrosinase tail mediates sorting to the lysosomal compartment in MDCK cells via a di-leucine and a tyrosine-based signal. J. Cell. Sci. 112, 45–53.
Shiba T., Takatsu H., Nogi T., et al. (2002). Structural basis for recognition of acidic-cluster dileucine sequence by GGA1. Nature 415, 937–941.
Misra S., Puertollano R., Kato Y., Bonifacino J. S., and Hurley J. H. (2002). Structural basis for acidic-cluster-dileucine sorting-signal recognition by VHS domains. Nature 415, 933–937.
Stahn R., Maier K. -P., and Hannig K. (1970). A new method for the preparation of rat liver lysosomes. Separation of cell organelles of rat liver by carrier-free continuous electrophoresis. J. Cell Biol. 46, 576–591.
Canut H., Bauer J., and Weber G. (1999). Separation of plant membranes by electromigration techniques. J. Chromatog. B., Biomed. Sci. Applic. 722, 121–139.
Volkl A. and Mohr H. (1999). Peroxisome subpopulations of the rat liver. Isolation by immune free flow electrophoresis. J. Histochem. Cytochem. 47, 1111–1118
Bagshaw R. D., Pasternak S. H., Mahuran D. J., and Callahan J. W. (2003). Nicastrin is a resident lysosomal membrane protein. Biochem. Biophys. Res. Commun. 300, 615–618.
Pasternak S. H., Bagshaw R. D., Guiral M., et al. (2003). Presenilin-1, Nicastrin, Amyloid Precursor Protein, and gamma-secretase activity are co-localized in the lysosomal membrane. J. Biol. Chem. 278, 26,687–26,694.
Chataway T. K., Whittle A. M., Lewis M. D., et al. (1998). Development of a two-dimensional gel electrophoresis database of human lysosomal proteins. Electrophoresis 19, 834–836.
Journet A., Chapel A., Kieffer S., Louwagie M., Luche S., and Garin J. (2000). Towards a human repertoire of monocytic lysosomal proteins. Electrophoresis 21, 3411–3419.
Bagshaw R., Callahan J. W., and Mahuran D. (2000). Lysosomal proteomics using 2D-gels and mass spectrometry. J. Inher. Metab. Dis. 23, 214.
Beruter J., Colombo J. P., and Bachmann C. (1978). Purification and properties of arginase from human liver and erythrocytes. Biochem. J. 175, 449–454.
Lu M., Sautin Y. Y., Holliday L. S., and Gluck S. L. (2004). The glycolytic enzyme aldolase mediates assembly, expression, and activity of vacuolar H+-ATPase. J. Biol. Chem. 279, 8732–8739.
Chevallet M., Santoni V., Poinas A., et al. (1998). New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis 19, 1901–1909.
Hippler M., Klein J., Fink A., Allinger T., and Hoerth P. (2001). Towards functional proteomics of membrane protein complexes: analysis of thylakoid membranes from Chlamydomonas reinhardtii. Plant J. 28, 595–606.
Bagshaw R. D., Mahuran D. J., and Callahan J. W. (2005). A proteomics analysis of lysosomal integral-membrane proteins reveals the diverse composition of the organelle. Molec. Cell Proteom. 4, 133–143.
Dell’Angelica E. C. (2003). Melanosome biogenesis: shedding light on the origin of an obscure organelle. Trends Cell Biol. 13, 503–506.
Di Pietro S. M., Falcon-Perez J. M., and Dell’Angelica E. C. (2004). Characterization of BLOC-2, a complex containing the Hermansky-Pudlak syndrome proteins HPS3, HPS5 and HPS6. Traffic 5, 276–283.
Nazarian R., Falcon-Perez J. M., and Dell’Angelica E. C. (2004). Biogenesis of lysosome-related organelles complex 3 (BLOC-3): a complex containing the Hermansky-Pudlak syndrome (HPS) proteins HPS1 and HPS4. Proc. Natl. Acad. Sci. USA 100, 8770–8775.
Verhoeven K., De Jonghe P., Coen K., et al. (2003). Mutations in the small GTP-ase late endosomal protein RAB7 cause Charcot-Marie-Tooth type 2B neuropathy. Am. J. Hum. Genet. 72, 722–727.
Pfeffer S. (2003). Membrane domains in the secretory and endocytic pathways. Cell 112, 507–517.
Pasqualato S., Renault L., and Cherfils J. (2002). Arf, Arl, Arp and Sar proteins: a family of GTP-binding proteins with a structural device for ‘front-back’ communication. EMBO Reports 3, 1035–1041.
Vernoud V., Horton A. C., Yang Z., and Nielsen E. (2003). Analysis of the small GTPase gene superfamily of Arabidopsis. Plant Physiol. 131, 1191–1208.
Riederer M. A., Soldati T., Shapiro A. D., Lin J., and Pfeffer S. R. (1994). Lysosome biogenesis requires Rab9 function and receptor recycling from endosomes to the trans-Golgi network. J. Cell Biol. 125, 573–582.
Lombardi D., Soldati T., Riederer M. A., Goda Y., Zerial M., and Pfeffer S. R. (1993). Rab9 functions in transport between late endosomes and the trans Golgi network. EMBO J 12, 677–682.
Arai K., Yoshida S., Naito S., and Ohkuma S. (2002). GTPgammaS-stimulated lysosomal lysis dependent of the assembly of adaptor proteins on lysosome. Biol. Pharm. Bull. 25, 1125–1128.
Sai Y., Matsuda T., Arai K., and Ohkuma S. (1998). Disintegration of lysosomes mediated by GTPgammaS-treated cytosol: possible involvement of phospholipases. J. Biochem. (Tokyo) 123, 630–636.
Jones D. H., Bax B., Fensome A., and Cockcroft S. (1999). ADP ribosylation factor 1 mutants identify a phospholipase D effector region and reveal that phospholipase D participates in lysosomal secretion but is not sufficient for recruitment of coatomer I. Biochem. J. 341, 185–192.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bagshaw, R.D., Mahuran, D.J. & Callahan, J.W. Lysosomal membrane proteomics and biogenesis of lysosomes. Mol Neurobiol 32, 27–41 (2005). https://doi.org/10.1385/MN:32:1:027
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1385/MN:32:1:027