Alternative Translation Initiation Produces Synaptic Organizer Proteoforms with Distinct Localization and Functions

Overview

Journal bioRxiv

Date 2024 Feb 26

PMID 38405936

Authors

Paul Jongseo Lee

Alexa R Soares

Yu Sun

Caroline Fai

Marina R Picciotto

Junjie U Guo

Affiliations

Soon will be listed here.

Abstract

While previous studies suggest that many mRNAs contain more than one translation initiation site (TIS), the biological significance of most alternative TISs and their corresponding protein isoforms (proteoforms) remains undetermined. Here we show that alternative translation initiation at a CUG and an AUG TIS in neuronal pentraxin receptor (NPR) mRNA produces two proteoforms, and their relative abundance is regulated by both neuronal activity as well as an adjacent RNA secondary structure. Downstream AUG initiation transforms the N-terminal transmembrane domain into a signal peptide, thereby converting NPR to a secreted factor sufficient to promote synaptic clustering of AMPA-type glutamate receptors. Changing the relative proteoform ratio, but not the overall NPR abundance reduces AMPA receptor in parvalbumin (PV)-positive interneurons and induces changes in learning behaviors in mice. In addition to NPR, N-terminal extensions of C1q-like synaptic organizers, mediated by upstream AUU start codons, anchor these otherwise secreted factors to the membrane. Thus, our results uncovered the plasticity of N-terminal signal sequences regulated by alternative TIS usage as a widespread mechanism to diversify protein localization and functions.

References

Yau J, Chaichim C, Power J, McNally G . The Roles of Basolateral Amygdala Parvalbumin Neurons in Fear Learning. J Neurosci. 2021; 41(44):9223-9234. PMC: 8570827. DOI: 10.1523/JNEUROSCI.2461-20.2021. View

Loughran G, Chou M, Ivanov I, Jungreis I, Kellis M, Kiran A . Evidence of efficient stop codon readthrough in four mammalian genes. Nucleic Acids Res. 2014; 42(14):8928-38. PMC: 4132726. DOI: 10.1093/nar/gku608. View

Tsang M, Cheeseman I . Alternative CDC20 translational isoforms tune mitotic arrest duration. Nature. 2023; 617(7959):154-161. PMC: 10461078. DOI: 10.1038/s41586-023-05943-7. View

Lee S, Wei M, Zhang C, Maxeiner S, Pak C, Calado Botelho S . Presynaptic Neuronal Pentraxin Receptor Organizes Excitatory and Inhibitory Synapses. J Neurosci. 2016; 37(5):1062-1080. PMC: 5296791. DOI: 10.1523/JNEUROSCI.2768-16.2016. View

Lee S, Liu B, Lee S, Huang S, Shen B, Qian S . Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc Natl Acad Sci U S A. 2012; 109(37):E2424-32. PMC: 3443142. DOI: 10.1073/pnas.1207846109. View

Matsuda K, Budisantoso T, Mitakidis N, Sugaya Y, Miura E, Kakegawa W . Transsynaptic Modulation of Kainate Receptor Functions by C1q-like Proteins. Neuron. 2016; 90(4):752-67. DOI: 10.1016/j.neuron.2016.04.001. View

Kall L, Krogh A, Sonnhammer E . Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res. 2007; 35(Web Server issue):W429-32. PMC: 1933244. DOI: 10.1093/nar/gkm256. View

DODDS D, Omeis I, Cushman S, Helms J, Perin M . Neuronal pentraxin receptor, a novel putative integral membrane pentraxin that interacts with neuronal pentraxin 1 and 2 and taipoxin-associated calcium-binding protein 49. J Biol Chem. 1997; 272(34):21488-94. DOI: 10.1074/jbc.272.34.21488. View

Shatsky I, Terenin I, Smirnova V, Andreev D . Cap-Independent Translation: What's in a Name?. Trends Biochem Sci. 2018; 43(11):882-895. DOI: 10.1016/j.tibs.2018.04.011. View

10.

Bolliger M, Martinelli D, Sudhof T . The cell-adhesion G protein-coupled receptor BAI3 is a high-affinity receptor for C1q-like proteins. Proc Natl Acad Sci U S A. 2011; 108(6):2534-9. PMC: 3038708. DOI: 10.1073/pnas.1019577108. View

11.

Williams C, Jan C, Weissman J . Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. Science. 2014; 346(6210):748-51. PMC: 4263316. DOI: 10.1126/science.1257522. View

12.

Chang M, Park J, Pelkey K, Grabenstatter H, Xu D, Linden D . Narp regulates homeostatic scaling of excitatory synapses on parvalbumin-expressing interneurons. Nat Neurosci. 2010; 13(9):1090-7. PMC: 2949072. DOI: 10.1038/nn.2621. View

13.

Xu D, Hopf C, Reddy R, Cho R, Guo L, Lanahan A . Narp and NP1 form heterocomplexes that function in developmental and activity-dependent synaptic plasticity. Neuron. 2003; 39(3):513-28. DOI: 10.1016/s0896-6273(03)00463-x. View

14.

Wang J, Shin B, Alvarado C, Kim J, Bohlen J, Dever T . Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation. Cell. 2022; 185(24):4474-4487.e17. PMC: 9691599. DOI: 10.1016/j.cell.2022.10.005. View

15.

Cho R, Park J, Wolff S, Xu D, Hopf C, Kim J . mGluR1/5-dependent long-term depression requires the regulated ectodomain cleavage of neuronal pentraxin NPR by TACE. Neuron. 2008; 57(6):858-71. PMC: 2701195. DOI: 10.1016/j.neuron.2008.01.010. View

16.

Ingolia N, Brar G, Rouskin S, McGeachy A, Weissman J . The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012; 7(8):1534-50. PMC: 3535016. DOI: 10.1038/nprot.2012.086. View

17.

Kazak L, Reyes A, Duncan A, Rorbach J, Wood S, Brea-Calvo G . Alternative translation initiation augments the human mitochondrial proteome. Nucleic Acids Res. 2013; 41(4):2354-69. PMC: 3575844. DOI: 10.1093/nar/gks1347. View

18.

Gruber A, Lorenz R, Bernhart S, Neubock R, Hofacker I . The Vienna RNA websuite. Nucleic Acids Res. 2008; 36(Web Server issue):W70-4. PMC: 2447809. DOI: 10.1093/nar/gkn188. View

19.

Atkins J, Loughran G, Bhatt P, Firth A, Baranov P . Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res. 2016; 44(15):7007-78. PMC: 5009743. DOI: 10.1093/nar/gkw530. View

20.

Pelkey K, Barksdale E, Craig M, Yuan X, Sukumaran M, Vargish G . Pentraxins coordinate excitatory synapse maturation and circuit integration of parvalbumin interneurons. Neuron. 2015; 85(6):1257-72. PMC: 4368480. DOI: 10.1016/j.neuron.2015.02.020. View