Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Functional dependence of neuroligin on a new non-PDZ intracellular domain


Neuroligins, a family of postsynaptic adhesion molecules, are important in synaptogenesis through a well-characterized trans-synaptic interaction with neurexin. In addition, neuroligins are thought to drive postsynaptic assembly through binding of their intracellular domain to PSD-95. However, there is little direct evidence to support the functional necessity of the neuroligin intracellular domain in postsynaptic development. We found that presence of endogenous neuroligin obscured the study of exogenous mutated neuroligin. We therefore used chained microRNAs in rat organotypic hippocampal slices to generate a reduced background of endogenous neuroligin. On this reduced background, we found that neuroligin function was critically dependent on the cytoplasmic tail. However, this function required neither the PDZ ligand nor any other previously described cytoplasmic binding domain, but rather required a previously unknown conserved region. Mutation of a single critical residue in this region inhibited neuroligin-mediated excitatory synaptic potentiation. Finally, we found a functional distinction between neuroligins 1 and 3.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Knockdown of neuroligin family necessary for functional study of cytoplasmic tail.
Figure 2: Replacement of endogenous NLGNs with wild-type and mutated NLGN3 reveals that AMPAR enhancement is dependent on a single residue in the cytoplasmic tail.
Figure 3: Critical region identified in NLGN3 is also crucial for the function of NLGN1 and NLGN4.
Figure 4: Mutation of the critical residue does not affect inhibitory synapses.
Figure 5: The effects of neuroligin on excitatory synapses are independent of excitatory synaptic activity.
Figure 6: Mechanism of synaptic enhancement by neuroligins and specific deficits of the mutant.


  1. 1

    Washbourne, P. et al. Cell adhesion molecules in synapse formation. J. Neurosci. 24, 9244–9249 (2004).

    CAS  Article  Google Scholar 

  2. 2

    Yamagata, M., Sanes, J.R. & Weiner, J.A. Synaptic adhesion molecules. Curr. Opin. Cell Biol. 15, 621–632 (2003).

    CAS  Article  Google Scholar 

  3. 3

    Dean, C. & Dresbach, T. Neuroligins and neurexins: linking cell adhesion, synapse formation and cognitive function. Trends Neurosci. 29, 21–29 (2006).

    CAS  Article  Google Scholar 

  4. 4

    de Wit, J. et al. LRRTM2 interacts with Neurexin1 and regulates excitatory synapse formation. Neuron 64, 799–806 (2009).

    CAS  Article  Google Scholar 

  5. 5

    Südhof, T.C. Neuroligins and neurexins link synaptic function to cognitive disease. Nature 455, 903–911 (2008).

    Article  Google Scholar 

  6. 6

    Chih, B., Engelman, H. & Scheiffele, P. Control of excitatory and inhibitory synapse formation by neuroligins. Science 307, 1324–1328 (2005).

    CAS  Article  Google Scholar 

  7. 7

    Song, J.Y., Ichtchenko, K., Sudhof, T.C. & Brose, N. Neuroligin 1 is a postsynaptic cell-adhesion molecule of excitatory synapses. Proc. Natl. Acad. Sci. USA 96, 1100–1105 (1999).

    CAS  Article  Google Scholar 

  8. 8

    Wittenmayer, N. et al. Postsynaptic Neuroligin1 regulates presynaptic maturation. Proc. Natl. Acad. Sci. USA 106, 13564–13569 (2009).

    CAS  Article  Google Scholar 

  9. 9

    Graf, E.R., Zhang, X., Jin, S.X., Linhoff, M.W. & Craig, A.M. Neurexins induce differentiation of GABA and glutamate postsynaptic specializations via neuroligins. Cell 119, 1013–1026 (2004).

    CAS  Article  Google Scholar 

  10. 10

    Nam, C.I. & Chen, L. Postsynaptic assembly induced by neurexin-neuroligin interaction and neurotransmitter. Proc. Natl. Acad. Sci. USA 102, 6137–6142 (2005).

    CAS  Article  Google Scholar 

  11. 11

    Fu, Z., Washbourne, P., Ortinski, P. & Vicini, S. Functional excitatory synapses in HEK293 cells expressing neuroligin and glutamate receptors. J. Neurophysiol. 90, 3950–3957 (2003).

    CAS  Article  Google Scholar 

  12. 12

    Scheiffele, P., Fan, J., Choih, J., Fetter, R. & Serafini, T. Neuroligin expressed in non-neuronal cells triggers presynaptic development in contacting axons. Cell 101, 657–669 (2000).

    CAS  Article  Google Scholar 

  13. 13

    Daoud, H. et al. Autism and nonsyndromic mental retardation associated with a de novo mutation in the NLGN4X gene promoter causing an increased expression level. Biol. Psychiatry 66, 906–910 (2009).

    CAS  Article  Google Scholar 

  14. 14

    Lawson-Yuen, A., Saldivar, J.S., Sommer, S. & Picker, J. Familial deletion within NLGN4 associated with autism and Tourette syndrome. Eur. J. Hum. Genet. 16, 614–618 (2008).

    CAS  Article  Google Scholar 

  15. 15

    Jamain, S. et al. Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. Nat. Genet. 34, 27–29 (2003).

    CAS  Article  Google Scholar 

  16. 16

    Blundell, J. et al. Neuroligin-1 deletion results in impaired spatial memory and increased repetitive behavior. J. Neurosci. 30, 2115–2129 (2010).

    CAS  Article  Google Scholar 

  17. 17

    Kim, J. et al. Neuroligin-1 is required for normal expression of LTP and associative fear memory in the amygdala of adult animals. Proc. Natl. Acad. Sci. USA 105, 9087–9092 (2008).

    CAS  Article  Google Scholar 

  18. 18

    Radyushkin, K. et al. Neuroligin-3-deficient mice: model of a monogenic heritable form of autism with an olfactory deficit. Genes Brain Behav. 8, 416–425 (2009).

    CAS  Article  Google Scholar 

  19. 19

    Araç, D. et al. Structures of neuroligin-1 and the neuroligin-1/neurexin-1 beta complex reveal specific protein-protein and protein-Ca2+ interactions. Neuron 56, 992–1003 (2007).

    Article  Google Scholar 

  20. 20

    Fabrichny, I.P. et al. Structural analysis of the synaptic protein neuroligin and its beta-neurexin complex: determinants for folding and cell adhesion. Neuron 56, 979–991 (2007).

    CAS  Article  Google Scholar 

  21. 21

    Irie, M. et al. Binding of neuroligins to PSD-95. Science 277, 1511–1515 (1997).

    CAS  Article  Google Scholar 

  22. 22

    Iida, J., Hirabayashi, S., Sato, Y. & Hata, Y. Synaptic scaffolding molecule is involved in the synaptic clustering of neuroligin. Mol. Cell. Neurosci. 27, 497–508 (2004).

    CAS  Article  Google Scholar 

  23. 23

    Poulopoulos, A. et al. Neuroligin 2 drives postsynaptic assembly at perisomatic inhibitory synapses through gephyrin and collybistin. Neuron 63, 628–642 (2009).

    CAS  Article  Google Scholar 

  24. 24

    Varoqueaux, F., Jamain, S. & Brose, N. Neuroligin 2 is exclusively localized to inhibitory synapses. Eur. J. Cell Biol. 83, 449–456 (2004).

    CAS  Article  Google Scholar 

  25. 25

    Levinson, J.N. et al. Neuroligins mediate excitatory and inhibitory synapse formation: involvement of PSD-95 and neurexin-1beta in neuroligin-induced synaptic specificity. J. Biol. Chem. 280, 17312–17319 (2005).

    CAS  Article  Google Scholar 

  26. 26

    Budreck, E.C. & Scheiffele, P. Neuroligin-3 is a neuronal adhesion protein at GABAergic and glutamatergic synapses. Eur. J. Neurosci. 26, 1738–1748 (2007).

    Article  Google Scholar 

  27. 27

    Chubykin, A.A. et al. Activity-dependent validation of excitatory versus inhibitory synapses by neuroligin-1 versus neuroligin-2. Neuron 54, 919–931 (2007).

    CAS  Article  Google Scholar 

  28. 28

    Futai, K. et al. Retrograde modulation of presynaptic release probability through signaling mediated by PSD-95-neuroligin. Nat. Neurosci. 10, 186–195 (2007).

    CAS  Article  Google Scholar 

  29. 29

    Prange, O., Wong, T.P., Gerrow, K., Wang, Y.T. & El-Husseini, A. A balance between excitatory and inhibitory synapses is controlled by PSD-95 and neuroligin. Proc. Natl. Acad. Sci. USA 101, 13915–13920 (2004).

    CAS  Article  Google Scholar 

  30. 30

    Bolliger, M.F. et al. Unusually rapid evolution of Neuroligin-4 in mice. Proc. Natl. Acad. Sci. USA 105, 6421–6426 (2008).

    CAS  Article  Google Scholar 

  31. 31

    Ko, J. et al. Neuroligin-1 performs neurexin-dependent and neurexin-independent functions in synapse validation. EMBO J. 28, 3244–3255 (2009).

    CAS  Article  Google Scholar 

  32. 32

    Dresbach, T., Neeb, A., Meyer, G., Gundelfinger, E.D. & Brose, N. Synaptic targeting of neuroligin is independent of neurexin and SAP90/PSD95 binding. Mol. Cell. Neurosci. 27, 227–235 (2004).

    CAS  Article  Google Scholar 

  33. 33

    Dean, C. et al. Neurexin mediates the assembly of presynaptic terminals. Nat. Neurosci. 6, 708–716 (2003).

    CAS  Article  Google Scholar 

  34. 34

    Varoqueaux, F. et al. Neuroligins determine synapse maturation and function. Neuron 51, 741–754 (2006).

    CAS  Article  Google Scholar 

  35. 35

    Chen, S.X., Tari, P.K., She, K. & Haas, K. Neurexin-neuroligin cell adhesion complexes contribute to synaptotropic dendritogenesis via growth stabilization mechanisms in vivo. Neuron 67, 967–983 (2010).

    CAS  Article  Google Scholar 

  36. 36

    Zhang, C. et al. A neuroligin-4 missense mutation associated with autism impairs neuroligin-4 folding and endoplasmic reticulum export. J. Neurosci. 29, 10843–10854 (2009).

    CAS  Article  Google Scholar 

  37. 37

    Heine, M. et al. Activity-independent and subunit-specific recruitment of functional AMPA receptors at neurexin/neuroligin contacts. Proc. Natl. Acad. Sci. USA 105, 20947–20952 (2008).

    CAS  Article  Google Scholar 

  38. 38

    Levinson, J.N. & El-Husseini, A. Building excitatory and inhibitory synapses: balancing neuroligin partnerships. Neuron 48, 171–174 (2005).

    CAS  Article  Google Scholar 

  39. 39

    Gutierrez, R.C. et al. Altered synchrony and connectivity in neuronal networks expressing an autism-related mutation of neuroligin 3. Neuroscience 162, 208–221 (2009).

    CAS  Article  Google Scholar 

  40. 40

    Tabuchi, K. et al. A neuroligin-3 mutation implicated in autism increases inhibitory synaptic transmission in mice. Science 318, 71–76 (2007).

    CAS  Article  Google Scholar 

  41. 41

    Petralia, R.S. et al. Selective acquisition of AMPA receptors over postnatal development suggests a molecular basis for silent synapses. Nat. Neurosci. 2, 31–36 (1999).

    CAS  Article  Google Scholar 

  42. 42

    Kerchner, G.A. & Nicoll, R.A. Silent synapses and the emergence of a postsynaptic mechanism for LTP. Nat. Rev. Neurosci. 9, 813–825 (2008).

    CAS  Article  Google Scholar 

  43. 43

    Bredt, D.S. & Nicoll, R.A. AMPA receptor trafficking at excitatory synapses. Neuron 40, 361–379 (2003).

    CAS  Article  Google Scholar 

  44. 44

    Stan, A. et al. Essential cooperation of N-cadherin and neuroligin-1 in the transsynaptic control of vesicle accumulation. Proc. Natl. Acad. Sci. USA 107, 11116–11121 (2010).

    CAS  Article  Google Scholar 

  45. 45

    Barrow, S.L. et al. Neuroligin1: a cell adhesion molecule that recruits PSD-95 and NMDA receptors by distinct mechanisms during synaptogenesis. Neural Dev. 4, 17 (2009).

    Article  Google Scholar 

  46. 46

    Comoletti, D. et al. The Arg451Cys-neuroligin-3 mutation associated with autism reveals a defect in protein processing. J. Neurosci. 24, 4889–4893 (2004).

    CAS  Article  Google Scholar 

  47. 47

    Ko, J., Fuccillo, M.V., Malenka, R.C. & Sudhof, T.C. LRRTM2 functions as a neurexin ligand in promoting excitatory synapse formation. Neuron 64, 791–798 (2009).

    CAS  Article  Google Scholar 

  48. 48

    Linhoff, M.W. et al. An unbiased expression screen for synaptogenic proteins identifies the LRRTM protein family as synaptic organizers. Neuron 61, 734–749 (2009).

    CAS  Article  Google Scholar 

  49. 49

    Stoppini, L., Buchs, P.A. & Muller, D. A simple method for organotypic cultures of nervous tissue. J. Neurosci. Methods 37, 173–182 (1991).

    CAS  Article  Google Scholar 

  50. 50

    Suh, Y.H. et al. A neuronal role for SNAP-23 in postsynaptic glutamate receptor trafficking. Nat. Neurosci. 13, 338–343 (2010).

    CAS  Article  Google Scholar 

Download references


We thank A.M. Craig, T. Sudhof and F. Varoqueaux for neuroligin constructs. We are grateful to K. Bjorgan for technical assistance and all members of the Nicoll laboratory and E. Dreyfuss for discussion of and comments on the manuscript. This work was supported by grants from the US National Institute of Mental Health.

Author information




E.S. initiated the project and generated preliminary data. S.L.S. designed experiments, performed all electrophysiology and all imaging in slice, constructed all new constructs, produced virus, conducted data analysis and wrote the manuscript. T.H. and B.-S.C. performed all biochemical experiments. T.H. designed and carried out imaging in dissociated neurons. R.A.N. and K.W.R. supervised the project. R.A.N., K.W.R. and E.S. provided comments on the manuscript.

Corresponding author

Correspondence to Roger A Nicoll.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 2012 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Shipman, S., Schnell, E., Hirai, T. et al. Functional dependence of neuroligin on a new non-PDZ intracellular domain. Nat Neurosci 14, 718–726 (2011).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing