Skip to main content

Thank you for visiting nature.com. 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.

  • Letter
  • Published:

Molecular determinants and guided evolution of species-specific RNA editing

Nature volume 434, pages 409–413 (2005)Cite this article

Abstract

Most RNA editing systems are mechanistically diverse, informationally restorative, and scattershot in eukaryotic lineages1. In contrast, genetic recoding by adenosine-to-inosine RNA editing seems common in animals; usually, altering highly conserved or invariant coding positions in proteins2,3,4. Here I report striking variation between species in the recoding of synaptotagmin I (sytI). Fruitflies, mosquitoes and butterflies possess shared and species-specific sytI editing sites, all within a single exon. Honeybees, beetles and roaches do not edit sytI. The editing machinery is usually directed to modify particular adenosines by information stored in intron-mediated RNA structures5,6,7. Combining comparative genomics of 34 species with mutational analysis reveals that complex, multi-domain, pre-mRNA structures solely determine species-appropriate RNA editing. One of these is a previously unreported long-range pseudoknot. I show that small changes to intronic sequences, far removed from an editing site, can transfer the species specificity of editing between RNA substrates. Taken together, these data support a phylogeny of sytI gene editing spanning more than 250 million years of hexapod evolution. The results also provide models for the genesis of RNA editing sites through the stepwise addition of structural domains, or by short walks through sequence space from ancestral structures.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Species-specific genetic recoding of synaptotagmin I.
Figure 2: Drosophila sytI pre-mRNA forms a pseudoknot.
Figure 3: Structure of lepidopteran sytI editing site and heterologous editing by dADAR.
Figure 4: Guided evolution of species-specific RNA editing.

Similar content being viewed by others

References

  1. Bass, B. L. (ed.) RNA Editing (Oxford University Press, Oxford, 2001)

  2. Seeburg, P. & Hartner, J. Regulation of ion channel/neurotransmitter receptor function by RNA editing. Curr. Opin. Neurobiol. 13, 279–283 (2003)

    Article  CAS  Google Scholar 

  3. Hoopengardner, B., Bhalla, T., Staber, C. & Reenan, R. Nervous system targets of RNA editing identified by comparative genomics. Science 301, 832–836 (2003)

    Article  ADS  CAS  Google Scholar 

  4. Bhalla, T., Rosenthal, J. J., Holmgren, M. & Reenan, R. Control of human potassium channel inactivation by editing of a small mRNA hairpin. Nature Struct. Mol. Biol. 11, 950–956 (2004)

    Article  CAS  Google Scholar 

  5. Herb, A., Higuchi, M., Sprengel, R. & Seeburg, P. Q/R site editing in kainate receptor GluR5 and GluR6 pre-mRNAs requires distant intronic sequences. Proc. Natl Acad. Sci. USA 93, 1875–1880 (1996)

    Article  ADS  CAS  Google Scholar 

  6. Dawson, T., Sansam, C. & Emeson, R. Structure and sequence determinants required for the RNA editing of ADAR2 substrates. J. Biol. Chem. 279, 4941–4951 (2004)

    Article  CAS  Google Scholar 

  7. Higuchi, M. et al. RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell 75, 1361–1370 (1993)

    Article  CAS  Google Scholar 

  8. Bass, B. L. RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71, 817–846 (2002)

    Article  CAS  Google Scholar 

  9. Tonkin, L. A. et al. RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans . EMBO J. 21, 6025–6035 (2002)

    Article  CAS  Google Scholar 

  10. Palladino, M. J., Keegan, L. P., O'Connell, M. A. & Reenan, R. A. A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell 102, 437–449 (2000)

    Article  CAS  Google Scholar 

  11. Higuchi, M. et al. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 406, 78–81 (2000)

    Article  ADS  CAS  Google Scholar 

  12. Gurevich, I. et al. Altered editing of serotonin 2C receptor pre-mRNA in the prefrontal cortex of depressed suicide victims. Neuron 34, 349–356 (2002)

    Article  CAS  Google Scholar 

  13. Kawahara, Y. et al. Glutamate receptors: RNA editing and death of motor neurons. Nature 427, 801 (2004)

    Article  ADS  CAS  Google Scholar 

  14. Brusa, R. et al. Early-onset epilepsy and postnatal lethality associated with an editing-deficient GluR-B allele in mice. Science 270, 1677–1680 (1995)

    Article  ADS  CAS  Google Scholar 

  15. Vissel, B. et al. The role of RNA editing of kainate receptors in synaptic plasticity and seizures. Neuron 29, 217–227 (2001)

    Article  CAS  Google Scholar 

  16. Aronoff, R., Mellem, J. E., Maricq, A. V., Sprengel, R. & Seeburg, P. H. Neuronal toxicity in Caenorhabditis elegans from an editing site mutant in glutamate receptor channels. J. Neurosci. 24, 8135–8140 (2004)

    Article  CAS  Google Scholar 

  17. Hanrahan, C. J., Palladino, M. J., Ganetzky, B. & Reenan, R. A. RNA editing of the Drosophila para Na+ channel transcript. Evolutionary conservation and developmental regulation. Genetics 155, 1149–1160 (2000)

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Grauso, M., Reenan, R. A., Culetto, E. & Sattelle, D. B. Novel putative nicotinic acetylcholine receptor subunit genes, Dα5, Dα6 and Dα7, in Drosophila melanogaster identify a new and highly conserved target of adenosine deaminase acting on RNA-mediated A-to-I pre-mRNA editing. Genetics 160, 1519–1533 (2002)

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Lehmann, K. A. & Bass, B. L. The importance of internal loops within RNA substrates of ADAR1. J. Mol. Biol. 291, 1–13 (1999)

    Article  CAS  Google Scholar 

  20. Yoshihara, M. & Littleton, J. T. Synaptotagmin I functions as a calcium sensor to synchronize neurotransmitter release. Neuron 36, 897–908 (2002)

    Article  CAS  Google Scholar 

  21. Craxton, M. Genomic analysis of synaptotagmin genes. Genomics 77, 43–49 (2001)

    Article  CAS  Google Scholar 

  22. Mackler, J. M. & Reist, N. E. Mutations in the second C2 domain of synaptotagmin disrupt synaptic transmission at Drosophila neuromuscular junctions. J. Comp. Neurol. 436, 4–16 (2001)

    Article  CAS  Google Scholar 

  23. Chapman, E. R., Desai, R. C., Davis, A. F. & Tornehl, C. K. Delineation of the oligomerization, AP-2 binding, and synprint binding region of the C2B domain of synaptotagmin. J. Biol. Chem. 273, 32966–32972 (1998)

    Article  CAS  Google Scholar 

  24. Rickman, C. et al. Synaptotagmin interaction with the syntaxin/SNAP-25 dimer is mediated by an evolutionarily conserved motif and is sensitive to inositol hexakisphosphate. J. Biol. Chem. 279, 12574–12579 (2004)

    Article  CAS  Google Scholar 

  25. Grass, I., Thiel, S., Honing, S. & Haucke, V. Recognition of a basic AP-2 binding motif within the C2B domain of synaptotagmin is dependent on multimerization. J. Biol. Chem. 279, 54872–54880 (2004)

    Article  CAS  Google Scholar 

  26. Nakhost, A., Houeland, G., Blandford, V. E., Castellucci, V. F. & Sossin, W. S. Identification and characterization of a novel C2B splice variant of synaptotagmin I. J. Neurochem. 89, 354–363 (2004)

    Article  CAS  Google Scholar 

  27. Reenan, R., Hanrahan, C. & Ganetzky, B. The mle(napts) RNA helicase mutation in Drosophila results in a splicing catastrophe of the para Na+ channel transcript in a region of RNA editing. Neuron 25, 139–149 (2000)

    Article  CAS  Google Scholar 

  28. Aruscavage, P. & Bass, B. A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing. RNA 6, 257–269 (2000)

    Article  CAS  Google Scholar 

  29. Kung, S. S., Chen, Y. C., Lin, W. H., Chen, C. C. & Chow, W. Y. Q/R RNA editing of the AMPA receptor subunit 2 (GRIA2) transcript evolves no later than the appearance of cartilaginous fishes. FEBS Lett. 509, 277–281 (2001)

    Article  CAS  Google Scholar 

  30. Wheeler, W. C., Whiting, M., Wheeler, Q. D. & Carpernter, J. M. The phylogeny of the extant hexapod orders. Cladistics 17, 113–169 (2001)

    Article  Google Scholar 

Download references

Acknowledgements

I thank L. Reenan for discussions; B. Hoopengardner, T. Bhalla and A. Das for comments on the manuscript; B. Hoopengardner for sharing certain genomic DNA templates and for assistance with S2 cell culture; UCHC Molecular Core Facility staff for diligent sequencing efforts; and M. Lalande for his encouragement. This work was supported by grants from the National Science Foundation and National Institutes of Health (R.A.R.).

Author information

Authors and Affiliations

  1. Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut, 06030, USA

    Robert A. Reenan

Authors
  1. Robert A. Reenan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Robert A. Reenan.

Ethics declarations

Competing interests

The author declares that he has no competing financial interests.

Supplementary information

Supplementary Methods

This document contains methods sections: 1. Insects used in this study. 2. Cloning and sequencing of synaptotagmin orthologues. 3. Primers used in this study. (PDF 117 kb)

Supplementary Legends

This document contains the legends for Supplementary Figures S1 through S5. (PDF 66 kb)

Supplementary Table S1

Contains all species information on insects and molecular data on sytI editing status in tabular form. (PDF 74 kb)

Supplementary Figure S1

Sequence alignment of synaptotagmin I from Drosophila species. (PDF 3162 kb)

Supplementary Figure S2

Sequence alignment of synaptotagmin I from Lepidopteran species. (PDF 2694 kb)

Supplementary Figure S3

Variation of synaptotagmin I editing structure within Lepidoptera. (PDF 1209 kb)

Supplementary Figure S4

Sequence alignment of synaptotagmin I from Anopheles species. (PDF 2756 kb)

Supplementary Figure S5

Comparison of Drosophila and Anopheles pseudoknot structure. (PDF 322 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Reenan, R. Molecular determinants and guided evolution of species-specific RNA editing. Nature 434, 409–413 (2005). https://doi.org/10.1038/nature03364

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature03364

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

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