Unifying Nomenclature for the Isoforms of the Lysosomal Membrane Protein LAMP-2


Eeva-Liisa Eskelinen, eeva-liisa.eskelinen@helsinki.fi


The present nomenclature of the splice variants of the lysosome-associated membrane protein type 2 (LAMP-2) is confusing. The LAMP-2a isoform is uniformly named in human, chicken, and mouse, but the LAMP-2b and LAMP-2c isoforms are switched in human as compared with mouse and chicken. We propose to change the nomenclature of the chicken and mouse b and c isoforms to agree with that currently used for the human isoforms. To avoid confusion in the literature, we further propose to adopt the use of capital letters for the updated nomenclature of all the isoforms in all three species: LAMP-2A, LAMP-2B, and LAMP-2C.

Lysosomal Membrane Glycoproteins

Lysosomes are acidic, membrane-bound organelles rich in hydrolytic enzymes. Lysosomes are responsible for the degradation of macromolecules derived from the extracellular space through endocytosis or phagocytosis, as well as from the cytoplasm through autophagy. The limiting membrane of lysosomes has an important role in sequestering the potentially harmful hydrolytic enzymes from the rest of the cytoplasm [for review, see (1)]. The most abundant glycoproteins of this membrane were identified about 20 years ago as antigens to monoclonal or polyclonal antibodies. The lysosomal membrane glycoproteins lysosome-associated membrane protein type 1 (LAMP-1) and LAMP-2 were first described by the groups of Mellman (2), August (3), Fambrough (4), and Sandoval (5). The classification of the LAMPs was finally clarified after their cDNAs were cloned and sequenced by the laboratories of Fukuda and Carlsson (6), Fambrough (7), Kato (8), August (9), and Helenius (10). This family of proteins was given different names by the different groups, but the nomenclature used by the August group, LAMP-1 and LAMP-2, is the most widely used today. Alternative spellings for both LAMPs have been used in the literature: LAMP-1/LAMP1/Lamp-1/Lamp1/lamp-1/lamp1 and LAMP-2/LAMP2/Lamp-2/Lamp2/lamp-2/lamp2; these should be kept in mind when performing searches in PubMed or related databases. Synonyms for LAMP-1 include GpIIa, SGM110, lgp120, lgp107/LGP107, LIMP-III/LIMP III, lamp A, lgp-A/lgp A, P2B, CD107a/CD107α, and LEP100. Alternative names for LAMP-2 include AC17, lgp110, lgp96/LGP96/LGP 96, lgp95, LIMP-IV/LIMP IV, lamp B, lgp-B/lgp B, and CD107b/CD107β[for review, see (1,11–13)].

Both LAMP-1 and LAMP-2 are type 1 membrane proteins, consisting of a short (11–12 amino acids) cytoplasmic tail, one transmembrane domain, and a heavily glycosylated luminal domain (Figure 1A). The molecular mass of the polypeptide backbone of human LAMP-1 and LAMP-2 is 40–45 kDa; however, after glycosylation, the mass of the glycoproteins is approximately 120 kDa (14,15). Human LAMP-1 was estimated to have 18, and human LAMP-2 16, N-linked carbohydrate chains (14). The numbers of N-linked carbohydrate chains predicted from the cDNA sequences of LAMP-1 and LAMP-2 in different species range from 16 to 23. N-glycosylation seems to be important for the stability of the proteins in the lysosomal membrane (5,16). In addition, both LAMPs have O-linked carbohydrates in the ‘hinge’ region of the luminal domain (17).

Figure 1.

Schematic drawing of the structure of mouse lysosome-associated membrane protein (LAMP)-2.A)The four loops are formed by disulfide bridges. The zigzag in the middle of the luminal domain denotes the proline-rich hinge region. Forks represent N-glycosylation sites and small rings denote putative O-glycosylation sites. The gray bar represents the lysosomal membrane. Lysosome-associated membrane protein type 1 has a very similar structure.B)The exon structure and alternative splicing of mouse LAMP-2. The three isoforms have identical luminal domains but distinct transmembrane and cytoplasmic domains. The nomenclature of the splice variants (8A, 8B, and 8C) corresponds to the unified nomenclature presented in Figure 2B. The dark areas in the exons 8B, 8A, and 8C represent the polypeptide coding region. The alternative exons 8B and 8C contain 3′ noncoding regions, while the exon 8A only contains the coding region.

Both LAMPs were originally thought to protect the lysosomal membrane against the action of the hydrolytic enzymes. However, cells deficient in both LAMP-1 and LAMP-2 still have intact lysosomes, although the buoyant density of lysosomes is decreased (18). Deficiency of LAMP-1 causes only a very mild phenotype in mice (19), whereas deficiency of LAMP-2 leads to a more severe phenotype including the accumulation of late autophagic vacuoles in several tissues such as heart, muscle, liver, and pancreas (20). In humans, mutations in the gene encoding LAMP-2 are the cause of Danon disease, a fatal cardiomyopathy and myopathy associated with mental retardation. The disease is characterized by the accumulation of late autophagic vacuoles in the heart and skeletal muscle (21,22). Mice deficient in LAMP-2 replicate the human disease (20). In addition, the lack of LAMP-2, or both LAMP-1 and LAMP-2, leads to the accumulation of free cholesterol in late endosomes (18). LAMP-2 also has a specific function in chaperone-mediated autophagy, a direct transport of certain cytosolic proteins into lysosomes for degradation (23). LAMP-2 may function as a receptor on the lysosomal membrane to mediate the binding and transport of substrate proteins into lysosomes (24).

LAMP-2 Alternative Splicing

Alternative splicing of the LAMP-2 pre-mRNA leads to three different isoforms, which have identical luminal domains but differing transmembrane and cytoplasmic domains (25). The human LAMP-2 gene has nine exons. Exons one to eight, and part of exon 9, encode the luminal domain. The rest of exon 9 encodes the transmembrane and cytoplasmic domains. The human exon 9 undergoes alternative splicing, which produces the isoforms LAMP-2a and LAMP-2b (21,26). The human LAMP-2c isoform was added to PubMed database in 2004 (access number AY561849, D Zhou and JS Blum). The mouse LAMP-2 gene has eight exons, with exons one to seven encoding the luminal domain and the eighth exon encoding the transmembrane domain and cytoplasmic tail of the protein. The exon structure and alternative splicing of mouse LAMP-2 gene are presented in Figure 1B.

The LAMP-2 isoforms show different subcellular localization and tissue distribution patterns (26–28). The mRNA encoding one of the isoforms (human LAMP-2b) is particularly abundant in muscle, and its absence seems to be the causative defect of Danon disease (21). In addition, the LAMP-2a, but not the other isoforms, seems to function in chaperone-mediated autophagy (29). The LAMP-2a isoform was also recently shown to facilitate MHC class II presentation of cytoplasmic antigens, probably through chaperone-mediated autophagy (30). It is not known at present whether the human LAMP-2c isoform has specific functions.

LAMP-2's alternatively spliced isoforms were first described simultaneously for human (LAMP-2a and LAMP-2b) (26) and for chicken (LAMP-2a, LAMP-2b, and LAMP-2c) (25). Although the nomenclature of the human and chicken LAMP-2a isoforms was identical, the human LAMP-2b corresponded to the chicken LAMP-2c. The mouse isoforms were reported some years later (28), and the nomenclature of the mouse isoforms was fitted to that of the chicken. In addition, the authors proposed to rename the human LAMP-2b and LAMP-2c isoforms to match the chicken and mouse nomenclature. This proposal, however, was not widely adopted, and confusion persists (Figure 2A).

Figure 2.

The sequence of lysosome-associated membrane protein (LAMP)-2 cytoplasmic tail in isoforms that have been published or are available in the PubMed database. Panel A shows the current nomenclature of human, chicken, and mouse isoforms. The unified nomenclature suggested in this paper is presented in panelB.Panel C shows the published LAMP-2 sequences and their proposed nomenclature of dog, rat (8), hamster (31), and bovine LAMP-2, with the PubMed access numbers in parenthesis. Some of these are predicted amino acid sequences.

This issue was discussed in the recent 2005 Gordon Research Conference on ‘Autophagy in stress, development and disease’ in Il Ciocco, Italy, after a session on myopathies. Because a human disorder, Danon disease, was associated with the human LAMP-2b isoform, the participants recommended that the nomenclature of the chicken and mouse LAMP-2b and LAMP-2c isoforms should be switched and unified with the current human nomenclature. To avoid confusion with the already published papers, we further suggest using capital letters (A, B, and C) instead of the small letters (a, b, and c) for the LAMP-2 isoforms (Figure 2B). Lysosome-associated membrane protein type 2 splicing variants already described in other species, and future identified sequences, should be designated according to the new unified nomenclature (Figure 2B,C). We also recommend that the spelling of both LAMPs be unified: with capital letters and a hyphen, as first introduced by the August group (i.e. LAMP-1 and LAMP-2).


Juan Bonifacino (NICHD, NIH, Bethesda, USA) has expressed his support to this nomenclature proposal.