ReviewBAFF, APRIL and their receptors: Structure, function and signaling
Introduction
The TNF family ligands APRIL (CD256, TNFSF13) [1] and BAFF (also known as BLyS, TALL-1, CD257 and TNFSF13B) [2], [3], [4] interact with three TNFR family members, TACI (CD267, TNFRSF13B) [5], BAFF-R (also known as BR3, CD268 or TNFRSF17) [6], [7] and BCMA (CD269, TNFRSF13C) [8]. APRIL and TACI also bind independently to glycosaminoglycan structures such as those present in syndecan-1 (CD138), or other proteoglycans [9], [10], [11].
The interaction pattern between BAFF, APRIL and their receptors is both specific and redundant: BAFF-R binds to BAFF, BCMA binds to APRIL, and TACI binds to BAFF and APRIL. In addition, BCMA binds BAFF with weaker affinity. Despite this complexity, the function of individual members of this subfamily in the immune system is relatively well understood, in great part as a result of the generation of a panel of mouse mutants. Recent papers have reviewed these functions, e.g. [12], [13], [14]. The present review seeks to provide insight into three aspects of BAFF biology: description of the numerous splice variants described for the different members of the BAFF complex; binding specificities of BAFF-R, BCMA and TACI and the structural determinants underlying ligand selectivity; and a summary overview of the fragmentary information available concerning the signaling pathways engaged by BAFF and APRIL, in the context of their known functions.
The TNF family ligand BAFF is a Type II membrane-bound protein, which can be released as a soluble trimeric ligand upon proteolytic processing at a furin consensus site. In the human BAFF gene, exon 1 codes for the transmembrane domain and its flanking regions, exon 2 for the furin processing site, and exons 3–6 for the TNF homology domain (THD), which binds to receptors (Fig. 1, Fig. 2).
At neutral or basic pH, 20 trimers of soluble recombinant human BAFF associate into a 60-mer virus-like structure, which irreversibly dissociates into trimers at acidic pH, or when fused to N-terminal extensions such as a myc tag [15], [16] (Fig. 3C). This association is dependent on an extended loop, known as the “Flap”, that is unique to BAFF in the TNF family [15] (Fig. 3A and B). The physiological importance of the BAFF 60-mer is unclear, but it is a biologically active entity that can bind receptors and is moderately more active than trimers in the in vitro assays [15], [17]. Endogenously produced 60-mer BAFF has recently been detected in supernatants of an histiocytic cell line [17].
The gene for mouse BAFF contains an additional exon encoding a stretch of 30 amino acids located between the furin site and the THD (Fig. 1A). This extension is predicted to prevent 60-mer formation in the mouse, although this has not been formally demonstrated. In both species, alternative splice variants, in which exon 3 (exon 4 in the mouse) is skipped, generate an in-frame deletion of the first β-sheet of the THD to produce a splice variant called ΔBAFF (Fig. 1, Fig. 2, Fig. 3). The structural impact of this deletion is unknown, but does not seem to prevent surface expression and heteromerization of ΔBAFF with BAFF, yet appears to prevent release of the soluble form [18]. Transgenic mice expressing ΔBAFF in myeloid and dendritic cells display reduced B cell number and impaired T-dependent humoral responses, consistent with ΔBAFF being a dominant-negative inhibitor of BAFF [19]. The splicing event in mouse ΔBAFF creates a functional N-linked glycosylation site [18], which is interesting in view of the fact that gain of glycosylation can considerably affect the biological activity of extracellular proteins [20].
Failure to splice intron 1 in human BAFF [18], or alternative splicing to an acceptor site in intron 3 are relatively frequent events, but result in the production of no or prematurely terminated BAFF protein (Fig. 1, Fig. 2).
The architecture of the APRIL gene resembles that of BAFF (Fig. 1). However, APRIL does not form 60-mers, but possesses residues close to the furin processing site in exon 3 that are crucial for binding to glycosaminoglycans (Fig. 2). APRIL binds sulfated glycosaminoglycans at sites independent from those used to bind other receptors [9], [10]. The relevance of this binding is unclear, but may serve to accumulate and/or multimerize APRIL in the extracellular matrix or at the surface of syndecan-positive cells. It thus may facilitate access to its receptor TACI, which also interacts with syndecans [11], or to intracellular BCMA [21] upon syndecan internalization.
A rare splicing event combines exon 1 of human APRIL to an alternative acceptor site in exon 3, thus generating a predicted membrane-bound, uncleavable human APRIL with no binding to glycosaminoglycans (APRIL-δ) (Fig. 1, Fig. 2). Omission of exon 3 yields APRIL-β, an homologue of ΔBAFF that also lacks the first β-sheet of the THD [22], and by analogy with ΔBAFF may regulate APRIL activity in a dominant-negative manner [18] (Fig. 2, Fig. 4). APRIL-γ is generated by splicing of a cryptic intron in exon 6, resulting in a four amino acids C-terminal truncation that is replaced by a single residue, but this isoform has not been further studied [22] (Fig. 2, Fig. 4). No similar sequences have been reported or detected in ESTs of murine APRIL. Mouse APRIL does, however, exist as two variants differing by a single amino acid (Ala120) which are found at similar frequencies. This subtle sequence difference originates from alternative use of two splice acceptor sites only three nucleotides apart at the beginning of exon 4. A similar splicing event was previously reported in another TNF family member, EDA, whose variants differ by two amino acid residues only, yet display distinct receptor specificities [23]. In the case of mouse APRIL, both variants bind TACI and BCMA, and the only difference in receptor specificity was observed in the weak, but detectable, binding of the shorter APRIL variant to mouse BAFF-R (unpublished data) (Fig. 2B). This weak binding is, however, only observed in the mouse system and is unlikely to be physiologically relevant.
In both human and mouse genomes, the APRIL gene is located immediately 3′ of TWEAK, another TNF family ligand. An intergenic splicing event between exon 6 of TWEAK and exon 2 of APRIL generates human TWE-PRIL (Fig. 1A). Although this mRNA has been convincingly shown to exist at abundances close to that of APRIL in T cells and various cell lines [24], it is intriguing that there is currently no EST sequence in the NCBI database harboring this junction, whereas ESTs coding for regular APRIL (in the corresponding region) are abundant (Fig. 2A). However, mouse TWE-PRIL ESTs are present as two variants, with or without Ala120 (Fig. 2B). The genesis of mouse TWE-PRIL is very different from that of its human orthologue, as it uses unique splice sites within exon 7 of TWEAK and within exon 1 of APRIL (Fig. 1A). Despite this difference, both human and mouse TWE-PRIL contain the entire THD of APRIL, and are therefore expected to display the same receptor specificity as APRIL. Although TWE-PRIL has two furin consensus cleavage sites, the overexpressed form of human TWE-PRIL was resistant to cleavage, as was ΔBAFF [18], [24].
BAFF-R and BCMA (and TACI) lack a signal peptide and are therefore classified as Type III membrane proteins. Exon 1 encodes the ligand-binding domain (also called cysteine-rich domain or CRD), exon 2 the transmembrane domain and flanking regions, and exon 3 the intracellular domain (Fig. 1B). The intracellular domains of both BAFF-R and BCMA are strongly homologous over a short sequence of 18 amino acids, which in the case of BCMA contains a TRAF-binding consensus site (P/S/A/T-X-Q/E-E) (Fig. 2). BCMA is indeed known to bind several TRAFs [25], [26]. Although the TRAF signature is not conserved in BAFF-R, this region binds to TRAF3 with high selectivity [27], [28]. In the mutant A/WySnJ mouse, a 4.7 kb gene insertion event disrupts the 3′ end of the BAFF-R gene, including part of this conserved sequence, leading to defective BAFF-R signaling [7]. The use of alternative splice donor and acceptor sites in exons 1 and 3, respectively, give rise to different mouse BAFF-R isoforms. These insertions and deletions occur outside the ligand and TRAF3 binding sites (Fig. 1, Fig. 2). Omission of exon 2 in human BCMA generates a predicted soluble receptor, but in the absence of a signal peptide, this protein is not expected to be secreted (Fig. 2A).
The 3′ genomic organization of TACI is similar to that of BCMA and BAFF-R, but the ligand-binding region is duplicated in an extra 5′ exon. This first ligand-binding domain has a much weaker affinity for BAFF and APRIL than the second one [29]. In human TACI only, an additional 5′ exon encodes a short N-terminal sequence. This often permits skipping of exon 2 to produce a short form of TACI lacking the first ligand-binding domain. This short TACI binds BAFF and APRIL as efficiently as the long form [29] (Fig. 1, Fig. 2). Human TACI is also subject to rarer intergenic splicing events removing the transmembrane and intracellular domains to yield soluble forms of TACI. However, TACI being a Type III protein, these proteins are not predicted to be secreted (Fig. 2A).
In mouse TACI, the initiating methionine and CRD1 are in the same exon. Excision of CRD1 is not possible in mouse TACI as it is in the human protein, because the 5′ non-coding exons do not contain an ATG codon in frame with the exon containing CRD2 (Fig. 1B). However, one sequence of TACI indicates that the reverse event can take place, i.e. deletion of the second CRD after splicing of a cryptic intron within exon 3 (Fig. 1, Fig. 2). Curiously, most mouse TACI transcripts start from within intron 4 and continue with exons encoding the transmembrane and intracellular portions of TACI. However, these transcripts lack initiating methionines and therefore should not encode proteins (Fig. 1, Fig. 2). It is not known if these transcripts regulate TACI expression or fulfill other specific functions. A practical outcome is that studies aimed at evaluating murine TACI expression at the RNA level will be influenced by the choice of RT-PCR primers.
In conclusion, conserved splicing events are relatively few (ΔBAFF and to a certain extent TWE-PRIL). Most other splicing events are species-specific, and therefore unlikely to play major biological roles.
Determining the true affinities of BAFF and APRIL for their receptors is not trivial. Indeed, measures performed with dimeric receptor–Ig proteins are subject to significant but unpredictable avidity effects that increase the apparent affinity. The avidity component is however removed by use of monomeric receptors, and results of such experiments are shown in Table 1. The consensus is that, on the one hand, BAFF binds to BAFF-R and TACI with affinities in the nanomolar range, yet displays two to three order of magnitude weaker binding to BCMA. On the other hand, APRIL binds TACI and BCMA with high affinity (nanomolar range), but not at all to BAFF-R. When receptors are dimerized as Ig fusion proteins, all receptors efficiently bind ligands in the low to subnanomolar range, with the exception of BAFF-R that does not bind to APRIL (Table 1, and reviewed in [30]). In comparison, APRIL binding to heparan sulfate proteoglycans is weak (20–80 μM) [30]. Whether endogenous BAFF can signal through BCMA in vivo is not known, but will certainly depend on avidity effects. Clustering of membrane-bound BCMA, clustering of membrane-bound BAFF or occurrence of multimerized forms of soluble BAFF (60-mer), are potential factors that may affect the avidity of the BAFF–BCMA interaction in vivo.
The molecular determinants of BAFF and APRIL specificity for their receptors have been solved through a number of elegant structural and mutational studies. BCMA and BAFF-R differ from other TNF receptor family members in that they possess a single cysteine-rich domain (CRD), which is used to establish extensive contacts with a single ligand monomer within BAFF or APRIL trimers [29], [31], [32] (Fig. 3, Fig. 4). Although TACI contains two CRDs, only the second one is necessary and sufficient for high affinity binding to BAFF and APRIL, so that the mode of TACI interaction with APRIL and BAFF is essentially the same as that of BCMA or BAFF-R [29]. This is in sharp contrast to other family members that contain up to four CRDs, and establish two main contact areas at the interface between two ligand protomers (reviewed in [33]).
BCMA, TACI and BAFF-R show perfect structural conservation in a β-hairpin structure that fits in a binding pocket of BAFF and APRIL and constitutes the conserved core of the interaction (Fig. 5). The hairpin structure is followed by a helix–loop–helix motive that is strikingly different among receptors: its spatial orientation differs in BCMA and TACI, independently of receptor binding, and BAFF-R contains only the first helix (Fig. 5). In a first approximation, it can be said that the hairpin is crucial for ligand binding, and that the C-terminal domain defines ligand specificity. Systematic mutagenesis studies of the ligand-binding sequence of BAFF-R [34], BCMA [35] and TACI [29] led to the precise identification of residues dictating the ligand specificity. For example, an aromatic residue in the hairpin, present in BCMA and TACI, but not BAFF-R, is absolutely required for APRIL binding, but dispensable for BAFF binding (Fig. 5, F78/Y13/C24). Introduction of this hydrophobic residue in BAFF-R confers binding to APRIL [31]. BAFF-R contains an hydrophobic residue (Leu38) that favors binding to BAFF but is detrimental for APRIL, further explaining the exquisite specificity of BAFF-R for BAFF and not APRIL (Fig. 5, P95/R27/L38). The corresponding position in BCMA is occupied by an arginine, which has the reverse effect, i.e. favoring APRIL binding, but inhibiting the interaction with BAFF. BCMA also lacks an arginine in the hairpin that establishes specific contacts with BAFF but not APRIL, accounting for the weak affinity of BAFF for BCMA (Fig. 5, R84/H19/R30). Human BCMA contains an hydrophobic residue (Ile22) that favors BAFF binding, but is not required for APRIL binding (Fig. 5, I87/I22/V33). Interestingly, mutation of this residue to an arginine abrogates the BCMA–BAFF interaction without significantly affecting binding to APRIL [35]. Finally, TACI does not present residues which are detrimental for APRIL or BAFF binding, explaining its dual specificity [29]. However, the set of residues involved in BAFF or APRIL interaction with TACI is partially different (Fig. 5).
In conclusion, the complex binding specificities of the BAFF and APRIL ligands (Fig. 2) is now very well understood at the molecular level.
Section snippets
BAFF-R and BCMA are involved in B cell survival
B cells enter the spleen at an immature T1 stage and further differentiate through the immature T2 stage to either mature or marginal zone B cells (Fig. 6). During differentiation, the requirement for a functional B cell receptor (BCR) is highlighted in IgβΔC mice [36]. The BCR consists of a surface immunoglobulin, which has no signaling capacity, and of Igβ and Igα chains that signal through their cytoplasmic tails. Deletion of the cytoplasmic tail of Igβ (IgβΔC) abrogates development of B
Concluding remarks
The BAFF subfamily shows a fascinating complexity at the levels of protein expression, ligand receptor interactions, signaling and functional outcomes. The past few years have witnessed considerable progress in our molecular understanding of ligand receptor specificity, and on the function of individual receptors. Although key features of signaling events leading to B cell survival have been highlighted, we are still far away from a complete molecular understanding of these signaling events.
Acknowledgments
We thank Helen Everett for careful reading of the manuscript. This work was supported by grants from the Swiss National Science Foundation, including a grant from the NCCR (National Center of Competence in Research) Molecular Oncology.
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