Overview of Bai’s and Bai Complexes

Bai’s (for ‘brain-angiogenesis inhibitors’ - likely erroneously named) are adhesion-GPCRs (aGPCRs) that are encoded by three genes (ADGRB1-3 in humans, Adgrb1-3 in mice; proteins are referred to as Bai1-3)^1,2. Bai’s are composed of N-terminal extracellular adhesion domains (an NTD domain of unknown structure, 5 [in Bai1] or 4 [in Bai2 & 3] thrombospondin repeat [TSR] domains, and a ‘hormone-binding’ domain), a canonical GAIN domain, a typical 7-transmembrane region GPCR module, and a large cytoplasmic sequence (see Figure). GAIN domains are characteristic of aGPCRs and undergoes autoproteolysis³ to expose a possible tethered agonist. Immunoblotting of brain samples showed that the Bai3 GAIN domain is catalytically active³. In contrast to neurexins, latrophilins, and other synaptic adhesion molecules, little alternative splicing of Bai’s was detected.

Extracellularly, Bai’s interact with at least two families of ligands. The TSR3 domain of Bai1 and the corresponding TSR2 domain of Bai3 (but not of Bai2) bind to RTN4R’s, which are leucine-rich repeat adhesion proteins attached to the plasma membrane via a GPI-lipid anchor (see Figure)⁴. The NTDs of Bai2 and Bai3, but not Bai1, bind to C1ql proteins, which constitute a family of 4 secreted proteins comprised of N-terminal multimerization sequences and C-terminal C1q-like domains^5,6. C1ql proteins form dimers of trimers that are in themselves composed of trimers, resulting in an 18-mer bouquet like structure (see Figure)⁷.

Intracellularly, Bai’s interact with proteins of the ELMO family, which are multidomain signaling scaffold coupled to the rho-rac pathway⁸. Since Bai’s are also GPCRs, their molecular architecture suggests that they can induce parallel rho-rac and G-protein signaling.

Bai’s have been reported to perform a large number of functions in addition to the original observation that a proteolytic fragment of Bai’s may act as an angiogenesis inhibitor. Among others, Bai1 was proposed to act as a macrophage receptor for phosphatidylserine that mediates the clearing of apoptotic cells⁹, but the absence of Bai1 expression in macrophages¹⁰ as well as reports of many other phosphatidylserine receptors in macrophages (e.g., Siglecs, Trem2, CD47, etc.) argue against this notion. Similarly, Bai1 was proposed to mediate myoblast fusion¹¹, but the lack of a major muscle development phenotype in Bai1 KO mice suggests that this is not an essential function¹². In adult mice, Bai’s are almost exclusively expressed in neurons in the brain. Bai1 and Bai2 KO mice exhibit neuronal function defects that are likely due to a synaptic impairment^1,2, but the precise nature and mechanism of these defects remain incompletely understood. Only for Bai3 has a molecularly defined function been identified. Specifically, Bai3 and its C1ql ligands were shown to be essential for climbing fiber synapse formation in the cerebellum^6,13 and for formation of synapses formed by AON neurons on granule cells in the olfactory bulb¹⁴.

Knowledge gaps. Although Bai’s are likely important and although they probably perform many functions, Bai’s are poorly characterized. Their fundamental roles in brain are only partly investigated, the importance of their ligand binding activities has not yet been probed, and their mechanism of action as aGPCRs is unknown. For example, it is unclear if the Bai GAIN domain and tethered agonist are functionally important, or even if Bai’s act as GPCRs or only as adhesion molecules.

References

1.     Stephenson JR, Purcell RH, Hall RA (2014) The BAI subfamily of adhesion GPCRs: synaptic regulation and beyond. Trends Pharmacol. Sci. 35, 208-215.

2.     Duman JG, Tu YK, Tolias KF (2016) Emerging Roles of BAI Adhesion-GPCRs in Synapse Development and Plasticity. Neural Plast. 2016, 8301737. 

3.     Arac, D., Boucard, A.A., Bolliger, M.F., Nguyen, J., Soltis, M., Südhof, T.C., and Brunger, A.T. (2011) A Novel Evolutionarily Conserved Domain of Cell-Adhesion GPCRs Mediates Autoproteolysis. EMBO J. 31, 1364-1378.

4.     Wang, J., Miao, Y., Wicklein, R., Sun, Z., Wang, J., Jude, K.M., Fernandes, R.A., Merrill, S.A., Wernig, M., Garcia, K.C., and Südhof, T.C. (2021) RTN4/NoGo-Receptor Binding to BAI Adhesion-GPCRs Regulates Neuronal Development. Cell 184, 5869-5885.

5.     Bolliger, M.F., Martinelli, D.C., and Südhof, T.C. (2011) The cell-adhesion G-protein coupled receptor BAI3 is a high-affinity receptor for C1q-like proteins. Proc. Natl. Acad. Sci. USA 108, 2534-2539.

6.     Kakegawa W, Mitakidis N, Miura E, Abe M, Matsuda K, Takeo YH, Kohda K, Motohashi J, Takahashi A, Nagao S, Muramatsu S, Watanabe M, Sakimura K, Aricescu AR, Yuzaki M (2015) Anterograde C1ql1 signaling is required in order to determine and maintain a single-winner climbing fiber in the mouse cerebellum. Neuron 85, 316-329. 

7.     Ressl, S., Vu, B.K., Vivona, S., Martinelli, D.C., Südhof, T.C., and Brunger, A.T. (2015) Structures of C1q-like Proteins Reveal Unique Features among the C1q/TNF Superfamily. Structure 23, 688-699.

8.     Weng Z, Situ C, Lin L, Wu Z, Zhu J, Zhang R (2019) Structure of BAI1/ELMO2 complex reveals an action mechanism of adhesion GPCRs via ELMO family scaffolds. Nat Commun. 10, 51.

9.     Park D, Tosello-Trampont AC, Elliott MR, Lu M, Haney LB, Ma Z, Klibanov AL, Mandell JW, Ravichandran KS (2007) BAI1 is an engulfment receptor for apoptotic cells upstream of the ELMO/Dock180/Rac module. Nature 450, 430-434.

10.  Hsiao CC, van der Poel M, van Ham TJ, Hamann J (2019) Macrophages Do Not Express the Phagocytic Receptor BAI1/ADGRB1. Front. Immunol. 10, 962. 

11.  Hochreiter-Hufford AE, Lee CS, Kinchen JM, Sokolowski JD, Arandjelovic S, Call JA, Klibanov AL, Yan Z, Mandell JW, Ravichandran KS (2013) Phosphatidylserine receptor BAI1 and apoptotic cells as new promoters of myoblast fusion. Nature 497, 263-267. 

12.  Shiu FH, Wong JC, Yamamoto T, Lala T, Purcell RH, Owino S, Zhu D, Van Meir EG, Hall RA, Escayg A (2022) Mice lacking full length Adgrb1 (Bai1) exhibit social deficits, increased seizure susceptibility, and altered brain development. Exp. Neurol. 351, 113994. 

13.  Sigoillot SM, Iyer K, Binda F, González-Calvo I, Talleur M, Vodjdani G, Isope P, Selimi F (2015) The Secreted Protein C1QL1 and Its Receptor BAI3 Control the Synaptic Connectivity of Excitatory Inputs Converging on Cerebellar Purkinje Cells. Cell Rep. 10, 820-832.

14.  Wang, C.Y., Liu, Z., Ng, Y.H., and Südhof, T.C. (2020) A synaptic circuit required for acquisition but not recall of social transmission of food preference. Neuron 107, 144-157.

Bai-RTN4R complexes

Properties. RTN4Rs are GPI-anchored surface proteins comprising 9 leucine-rich repeats with N- and C-terminal cap sequences but no other domains. Three paralogous genes (RTN4R, RTN4RL1, and RTN4RL2) are expressed in mammals. RTN4R’s were named as ‘reticulon-4 receptors’ with the understanding that reticulon-4 serves as a ‘no-go’ signal in axonal growth and thereby hinders regeneration of axonal connections that have been lost, and that RTN4Rs are the receptors mediating this ‘no-go’ signal1. However, subsequent studies indicated that reticulon-4, an abundant endoplasmic reticulum protein, is probably not displayed on the cell surface and that RTN4Rs are unlikely receptors for reticulon-42.

Interactions. The only validated interactions of RTN4Rs are with Bai1 and Bai3 (ref. 3). However, given that RTN4Rs are GPI-anchored and have important neuronal functions, it seems likely that they form a tripartite complex with a third surface protein that is yet to be identified. The atomic structure of the RTN4R-Bai complex exhibits an unusual binding interface that is shaped by C-mannosylation of tryptophan and O-fucosylation of threonine in the Bai TSR-domains. This observation provides a physiological role for these unusual carbohydrate modifications typical of TSR domains3. 

Function. Deletion of RTN4RL1 or RTN4RL2 in human neurons caused three phenotypes: a decrease in synapse density and increases in dendritic and in axonal growth and arborization. Thus, RTN4R’s are likely regulators of multiple neuronal processes. The RTN4RL1/2 deletion phenotypes could be rescued by re-expression of WT but not of Bai-binding deficient RTN4RL’s3. Deletion of Bai’s in the mouse glia that form the substrates on which the human neurons are cultured replicated the axonal outgrowth phenotype but not the other phenotypes, suggesting that the function of RTN4RLs in dendritic outgrowth and synapse formation depend on binding to neuronal Bai’s, whereas their function in axonal outgrowth depends on binding to glial Bai’s3.

Knowledge gaps. Overall, little is known about RTN4Rs and their interaction with Bai’s except for their atomic structures. It is unclear whether RTN4Rs only act by binding to Bai’s or whether they have Bai-independent functions, and whether their Bai-dependent functions involve interactions with a third protein. Moreover, the relative differences among the three RTN4R paralogs in terms of functions and interactions have not been characterized.

References

1.    Schwab ME, Strittmatter SM (2014) Nogo limits neural plasticity and recovery from injury. Curr. Opin. Neurobiol. 27, 53-60.

2.    Voeltz GK, Prinz WA, Shibata Y, Rist JM, Rapoport TA (2006) A class of membrane proteins shaping the tubular endoplasmic reticulum. Cell 124, 573-586. 

3.    Wang, J., Miao, Y., Wicklein, R., Sun, Z., Wang, J., Jude, K.M., Fernandes, R.A., Merrill, S.A., Wernig, M., Garcia, K.C., and Südhof, T.C. (2021) RTN4/NoGo-Receptor Binding to BAI Adhesion-GPCRs Regulates Neuronal Development. Cell 184, 5869-5885.

Bai-C1ql protein complexes

Properties. C1ql’s are expressed from four genes (C1ql1-4). C1ql’s belong to a superfamily of secreted proteins that contain trimers of C1q-like domains, including the eponymous C1qA, C1qB, and C1qC proteins that constitute the final convergent step of the complement pathway (see Figure)1. C1ql’s stand out among secreted small C1q-domain proteins in that they contain both a characteristic cysteine-rich domain forming disulfide-bonded dimers and a collagen-like domain forming trimers2. As a result, C1ql’s assemble into large 18-meric complexes composed of dimers of trimers of trimeric C1ql protein subcomplexes (see Figure above on Bai’s). C1ql’s are primarily expressed in brain except for C1ql1 that is also present in peripheral tissues (especially kidney) and C1ql4 that is primarily expressed in male reproductive organs.

Interactions. C1ql’s bind to the NTD of Bai3 with high affinity3,4. In addition, C1ql’s were shown to bind to the SS5+ splice variant of Nrxn3 and to the NTD of kainate receptors5.

Function. Presynaptic deletion of C1ql1 or C1ql3 has been shown to diminish synapse densities in several brain regions, such as climbing-fiber synapses in cerebbellum4,6 and synapses formed by accessory olfactory nucleus neurons on granule cells in the olfactory bulb7,8. In these cases, deletions of Bai3 in the postsynaptic neurons resulted in the same phenotype as the presynaptic C1ql deletion. Moreover, deletion of C1ql2 and C1ql3 in dentate gyrus granule cells disorganizes mossy-fiber synapses, but in this case the phenotype was proposed to depend on C1ql-binding to Nrxn3 and kainate receptors5.

Knowledge gaps. The stoichiometry and structural mechanism of C1ql-binding to Bai3 is unclear, and the relation of this binding to RTN4R-binding to Bai3 or to C1ql-binding to Nrxn3 and kainate receptors is unknown. Moreover, it is unclear by what mechanism C1ql’s act in synapse formation. For example, is their multimerization essential?

References

1.     Yuzaki M (2017) The C1q complement family of synaptic organizers: not just complementary. Curr. Opin. Neurobiol. 45, 9-15. 

2.     Ressl, S., Vu, B.K., Vivona, S., Martinelli, D.C., Südhof, T.C., and Brunger, A.T. (2015) Structures of C1q-like Proteins Reveal Unique Features among the C1q/TNF Superfamily. Structure 23, 688-699.

3.     Bolliger, M.F., Martinelli, D.C., and Südhof, T.C. (2011) The cell-adhesion G-protein coupled receptor BAI3 is a high-affinity receptor for C1q-like proteins. Proc. Natl. Acad. Sci. USA 108, 2534-2539.

4.     Kakegawa W, Mitakidis N, Miura E, Abe M, Matsuda K, Takeo YH, Kohda K, Motohashi J, Takahashi A, Nagao S, Muramatsu S, Watanabe M, Sakimura K, Aricescu AR, Yuzaki M (2015) Anterograde C1ql1 signaling is required in order to determine and maintain a single-winner climbing fiber in the mouse cerebellum. Neuron 85, 316-329. 

5.     Matsuda K, Budisantoso T, Mitakidis N, Sugaya Y, Miura E, Kakegawa W, Yamasaki M, Konno K, Uchigashima M, Abe M, Watanabe I, Kano M, Watanabe M, Sakimura K, Aricescu AR, Yuzaki M (2016) Transsynaptic Modulation of Kainate Receptor Functions by C1q-like Proteins. Neuron 90, 752-767.

6.     Sigoillot SM, Iyer K, Binda F, González-Calvo I, Talleur M, Vodjdani G, Isope P, Selimi F (2015) The Secreted Protein C1QL1 and Its Receptor BAI3 Control the Synaptic Connectivity of Excitatory Inputs Converging on Cerebellar Purkinje Cells. Cell Rep. 10, 820-832.

7.     Wang, C.Y., Liu, Z., Ng, Y.H., and Südhof, T.C. (2020) A synaptic circuit required for acquisition but not recall of social transmission of food preference. Neuron 107, 144-157.

8.     Martinelli, D.C., Chew, K.S., Rohlmann, A., Lum, M.Y., Ressl, S., Hattar, S., Brunger, A.T., Missler, M., and Südhof, T.C. (2016) Expression of C1ql3 in Discrete Neuronal Populations Controls Efferent Synapse Numbers and Diverse Behaviors. Neuron 91, 1034-1051.

9.     Aimi T, Matsuda K, Yuzaki M (2023) C1ql1-Bai3 signaling is necessary for climbing fiber synapse formation in mature Purkinje cells in coordination with neuronal activity. Mol Brain 16, 61.