Olfactory receptor pseudo-pseudogenes

Abstract

Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes1. Although certain pseudogene-derived RNAs have regulatory roles2, and some pseudogene fragments are translated3, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, which reflect low selection pressures on loci no longer relevant to the fitness of a species4. Here we report the characterization of a pseudogene in the chemosensory variant ionotropic glutamate receptor repertoire5,6 of Drosophila sechellia, an insect endemic to the Seychelles that feeds almost exclusively on the ripe fruit of Morinda citrifolia7. This locus, D. sechellia Ir75a, bears a premature termination codon (PTC) that appears to be fixed in the population. However, D. sechellia Ir75a encodes a functional receptor, owing to efficient translational read-through of the PTC. Read-through is detected only in neurons and is independent of the type of termination codon, but depends on the sequence downstream of the PTC. Furthermore, although the intact Drosophila melanogaster Ir75a orthologue detects acetic acid—a chemical cue important for locating fermenting food8,9 found only at trace levels in Morinda fruit10D. sechellia Ir75a has evolved distinct odour-tuning properties through amino-acid changes in its ligand-binding domain. We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such ‘pseudo-pseudogenes’ could represent a widespread phenomenon.

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Figure 1: Ir75a encodes an acetic acid receptor in D. melanogaster and is a transcribed pseudogene in D. sechellia.
Figure 2: Translational read-through of the PTC in D. sechellia Ir75a permits production of a functional olfactory receptor.
Figure 3: Efficiency and tissue-specificity of translational read-through of the D. sechellia Ir75a PTC.
Figure 4: Molecular basis of the functional divergence of D. sechellia Ir75a.
Figure 5: Functional pseudogene alleles of other receptors in other species.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

Sequences of cloned ORFs have been deposited in GenBank under accession numbers: KX694388 (D. melanogaster Ir75a) and KX694389 (D. sechellia Ir75a).

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Acknowledgements

We acknowledge C. Carracedo, P. Casares, the Bloomington Drosophila Stock Center (NIH P40OD018537), the Drosophila Species Stock Center (UCSD), and the Developmental Studies Hybridoma Bank (NICHD of the NIH, University of Iowa) for reagents. We thank members of the Benton laboratory for discussions and comments on the manuscript. L.L.P.-G. was supported by a FEBS long-term fellowship; R.R. was supported by a Roche Research Foundation fellowship. J.R.A. was supported by a post-doctoral fellowship from Novartis Foundation for medical–biological research (12A14). M.D.P.’s laboratory was supported by the SNSF. Research in R.B.’s laboratory was supported by ERC Starting Independent Researcher and Consolidator Grants (205202 and 615094), an HFSP Young Investigator Award (RGY0073/2011) and the SNSF Nano-Tera Envirobot project (20NA21_143082).

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Authors

Contributions

L.L.P.-G. and R.B. conceived the project. L.L.P.-G., R.R., B.B. and M.D.P. designed experiments. L.L.P.-G., R.R., L.A. and R.B. generated reagents. L.L.P.-G. performed electrophysiology, bioinformatics and histology. R.R. performed electrophysiology and molecular analyses. B.B. generated protein models. L.A. performed histology. J.R.A. performed bioinformatics. L.L.P.-G., R.R., B.B., J.R.A. and R.B. analysed data. L.L.P.-G. and R.B. wrote the paper with input from all authors.

Corresponding author

Correspondence to Richard Benton.

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The authors declare no competing financial interests.

Additional information

Reviewer Information Nature thanks A. Jacobson, M. Stensmyr and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Figure 1 Quantification of efficiency and tissue-specificity of translational read-through of the D. sechellia Ir75a PTC.

Quantification of GFP staining in the cell bodies of neurons expressing different read-through reporter constructs in different populations of OSNs (see Figs 2, 3 for genotypes). GFP fluorescence levels were normalized by anti-Ir75a fluorescence levels in the Cy3 channel within each analysed cell. Box plots indicate the median and first and third quartile of the data. *P < 0.05, ***P < 0.0005, not significant (n.s.) P > 0.05 (all data analysed using pairwise Wilcoxon rank-sum test, Benjamini–Hochberg correction).

Extended Data Figure 2 Tissue specificity of translational read-through of the D. sechellia Ir75a PTC.

Immunofluorescence with anti-GFP (green) and the neuron nuclear marker anti-Elav (magenta) on whole-mount D. melanogaster antennae in which actin5C-GAL4 drives broad expression of D. sechellia Ir75a*214Q:GFP (UAS-DsIr75a*214Q:GFP/act5C-GAL4) or Ir75a:GFP (UAS-DsIr75a:GFP/act5C-GAL4). Arrowheads indicate examples of GFP-expressing, Elav-negative, non-neuronal cells that were observed in 6 out of 6 antennae expressing the control transgene lacking the PTC, and in 0 out of 6 antennae expressing the PTC-containing transgene. Note that the neuronal GFP signal of both transgenes is heterogeneous across the antenna, possibly because of the variable strength of driver expression and/or instability of the GFP-tagged receptors in heterologous neurons. Scale bars, 10 μm.

Extended Data Figure 3 Alignment of drosophilid Ir75a orthologues.

Protein-sequence alignment of D. melanogaster, D. simulans and D. sechellia Ir75a. Blue bars indicate the S1 and S2 lobes of the predicted LBD. The position of the PTC (X) is highlighted in yellow. Dark grey columns in the alignment highlight amino acids conserved only in two of the three species. Pink and red shading represents D. sechellia-specific amino acid changes within the LBD; red denotes the subset located in the internal cavity of the binding pocket (Fig. 4a). The locations of the peptide epitopes for the Ir75a antibodies are highlighted with green dashed boxes.

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Prieto-Godino, L., Rytz, R., Bargeton, B. et al. Olfactory receptor pseudo-pseudogenes. Nature 539, 93–97 (2016). https://doi.org/10.1038/nature19824

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