|Mutation Type||splice site (3 bp from exon)|
|Coordinate||86,547,526 bp (GRCm38)|
|Base Change||T ⇒ C (forward strand)|
|Gene Name||phosphodiesterase 6D, cGMP-specific, rod, delta|
|Chromosomal Location||86,542,994-86,582,629 bp (-)|
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the delta subunit of rod-specific photoreceptor phosphodiesterase (PDE), a key enzyme in the phototransduction cascade. A similar protein in cow functions in solubilizing membrane-bound PDE. In addition to its role in the PDE complex, the encoded protein is thought to bind to prenyl groups of proteins to target them to subcellular organelles called cilia. Mutations in this gene are associated with Joubert syndrome-22. Alternative splicing results in multiple splice variants. [provided by RefSeq, Mar 2014]
PHENOTYPE: Homozygous null mice exhibit progressive retinal degeneration with progressive loss of rod and cone neurons. [provided by MGI curators]
|Amino Acid Change|
|Institutional Source||Beutler Lab|
|Gene Model||predicted gene model for protein(s): [ENSMUSP00000027444 †] [ENSMUSP00000137956] [ENSMUSP00000137820 †] † probably from a misspliced transcript|
|Predicted Effect||probably null|
AA Change: T48A
|Predicted Effect||probably benign
PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Meta Mutation Damage Score||0.9755|
|Is this an essential gene?||Possibly nonessential (E-score: 0.323)|
|Candidate Explorer Status||CE: excellent candidate; Verification probability: 0.567; ML prob: 0.542; human score: 4.5|
Linkage Analysis Data
|Alleles Listed at MGI|
|Mode of Inheritance||Autosomal Recessive|
|Last Updated||2019-09-04 9:44 PM by Anne Murray|
|Record Created||2015-10-26 4:56 PM by Zhe Chen|
The costume phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R3084, some of which showed reduced body weights compared to wild-type littermates (Figure 1).
|Nature of Mutation|
Whole exome HiSeq sequencing of the G1 grandsire identified 43 mutations. The body weight phenotype was linked to a mutation in Pde6d: an A to G transition at base pair 86,547,526 (v38) on chromosome 1, or base pair 35,283 in the GenBank genomic region NC_000067 encoding Pde6d. Linkage was found with a recessive model of inheritance, wherein four variant homozygotes departed phenotypically from 19 homozygous reference mice and 22 heterozygous mice with a P value of 1.572 x 10-6 (Figure 2).
The effect of the mutation at the cDNA and protein level have not examined, but the mutation is predicted to result in skipping of the 89-nucleotide exon 2 (out of 5 total exons), resulting in a frame-shifted protein product beginning after amino acid 17 and coding of a premature stop codon at amino after 53 aberrant amino acids (at amino acid 70).
The donor splice site of intron 2, which is destroyed by the costume mutation, is indicated in blue lettering and the mutated nucleotide is indicated in red.
|Illustration of Mutations in
Gene & Protein
Pde6d encodes cGMP phosphodiesterase (PDE6δ; alternatively, PDEδ, PrBP/δ, or PDE6D), a member of the phosphodiesterase superfamily. The members of the phosphodiesterase superfamily regulate the concentrations of cAMP and cGMP in the cell (1).
PDE6δ is structurally similar to Rho GTPase guanine nucleotide dissociation inhibitor (RhoGDI) and UNC119 in that it forms an immunoglobulin-like β-sandwich fold composed of two β-sheets that form a hydrophobic pocket [Figure 3 & 4; (2); reviewed in (3)]. The N-terminal region of PDE6δ is an α-helix (α1), and a short 310 helix occurs in one of the loop regions [Figure 4; (4;5); PDB: 1KSG]. One β-sheet of the immunoglobulin-like β-sandwich fold is formed by four β-strands, and the other β-sheet is formed by five β-strands (5). The loop connecting β7 and β8 is disordered. The immunoglobulin-like β-sandwich fold mediates farnesyl (C15) and geranylgeranyl (C20) lipid binding (6).
The costume mutation is predicted to result in a frame-shifted protein that encodes a premature stop codon after amino acid 70.
PDE6δ is a chaperone involved in the transport of a number of prenylated proteins (Table 1) to several sites in the cell, but predominantly in the cilia (6;8;9). Prenylation is the covalent addition of farnesyl or geranylgeranyl isoprenoids to the cysteine of a CAAX (C = cysteine, A = aliphatic amino acid, X = any amino acid) box in target cytosolic proteins through a thioether bond by cytosolic prenyl transferases (10;11). The “X” in the CAAX box determines that nature of the lipid chain; a leucine at that residue specifies geranylgeranylation, while all other residues promote farnesylation.
Table 1. Known PDE6δ interacting proteins
During PDE6δ-mediated sorting of prenylated proteins, PDE6δ binds the cargo and sorts it into the appropriate cellular compartment. The high-affinity cargo is released by ARL3 in the cilia; low-affinity cargo is released by ARL2 into the entire cell. A retention signal facilitates the retention of the prenylated cargo at the appropriate location in the cell (12).
Mutations in PDE6D are associated with Joubert syndrome (OMIM# #615665), a ciliopathy caused by defects in ciliary biogenesis and/or function. One such mutation in PDE6D is a null allele that causes defective trafficking of INPP5E to cilia (14). Patients with the null PDE6D mutation exhibit polydactyly, microphthalmia (i.e., developmental disorder of the eye in which one or both eyes are abnormally small and have anatomic malformations), coloboma (i.e., congenital malformation of the eye causing defects in the lens, iris, or retina), and renal hypoplasia.
Pde6d-deficient (Pde6d-/-) mice were viable and fertile, but exhibited reduced body sizes early in life (15). The Pde6d-/- mice exhibited defective transport of GRK1, cone PDE6, and Tβγ to the outer segments of rod and cone photoreceptor of the retina, which caused a slowly progressive form of retinitis pigmentosa [reviewed in (3)]. Similar to the Pde6d-/- mice, the costume mice exhibit reduced body size/weights compared to wild-type littermates indicating that PDE6δcostume is a loss-of-function allele. The costume mice have not been examined for abnormalities of the retina.
1) 94°C 2:00
The following sequence of 760 nucleotides is amplified (chromosome 1, - strand):
1 agttcatgtc tcagatgtta tgtaacatgg tgtagattaa aaacctctgg agtcagctgg
Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.
1. Conti, M., and Beavo, J. (2007) Biochemistry and Physiology of Cyclic Nucleotide Phosphodiesterases: Essential Components in Cyclic Nucleotide Signaling. Annu Rev Biochem. 76, 481-511.
2. Hoffman, G. R., Nassar, N., and Cerione, R. A. (2000) Structure of the Rho Family GTP-Binding Protein Cdc42 in Complex with the Multifunctional Regulator RhoGDI. Cell. 100, 345-356.
3. Baehr, W. (2014) Membrane Protein Transport in Photoreceptors: The Function of PDEdelta: The Proctor Lecture. Invest Ophthalmol Vis Sci. 55, 8653-8666.
4. Zhang, H., Constantine, R., Frederick, J. M., and Baehr, W. (2012) The Prenyl-Binding Protein PrBP/delta: A Chaperone Participating in Intracellular Trafficking. Vision Res. 75, 19-25.
5. Hanzal-Bayer, M., Renault, L., Roversi, P., Wittinghofer, A., and Hillig, R. C. (2002) The Complex of Arl2-GTP and PDE Delta: From Structure to Function. EMBO J. 21, 2095-2106.
6. Zhang, H., Liu, X. H., Zhang, K., Chen, C. K., Frederick, J. M., Prestwich, G. D., and Baehr, W. (2004) Photoreceptor cGMP Phosphodiesterase Delta Subunit (PDEdelta) Functions as a Prenyl-Binding Protein. J Biol Chem. 279, 407-413.
7. Florio, S. K., Prusti, R. K., and Beavo, J. A. (1996) Solubilization of Membrane-Bound Rod Phosphodiesterase by the Rod Phosphodiesterase Recombinant Delta Subunit. J Biol Chem. 271, 24036-24047.
8. Ismail, S. A., Chen, Y. X., Rusinova, A., Chandra, A., Bierbaum, M., Gremer, L., Triola, G., Waldmann, H., Bastiaens, P. I., and Wittinghofer, A. (2011) Arl2-GTP and Arl3-GTP Regulate a GDI-Like Transport System for Farnesylated Cargo. Nat Chem Biol. 7, 942-949.
9. Cook, T. A., Ghomashchi, F., Gelb, M. H., Florio, S. K., and Beavo, J. A. (2000) Binding of the Delta Subunit to Rod Phosphodiesterase Catalytic Subunits Requires Methylated, Prenylated C-Termini of the Catalytic Subunits. Biochemistry. 39, 13516-13523.
10. Magee, T., and Seabra, M. C. (2005) Fatty Acylation and Prenylation of Proteins: What's Hot in Fat. Curr Opin Cell Biol. 17, 190-196.
11. Zhang, F. L., and Casey, P. J. (1996) Protein Prenylation: Molecular Mechanisms and Functional Consequences. Annu Rev Biochem. 65, 241-269.
12. Fansa, E. K., Kosling, S. K., Zent, E., Wittinghofer, A., and Ismail, S. (2016) PDE6delta-Mediated Sorting of INPP5E into the Cilium is Determined by Cargo-Carrier Affinity. Nat Commun. 7, 11366.
13. Humbert, M. C., Weihbrecht, K., Searby, C. C., Li, Y., Pope, R. M., Sheffield, V. C., and Seo, S. (2012) ARL13B, PDE6D, and CEP164 Form a Functional Network for INPP5E Ciliary Targeting. Proc Natl Acad Sci U S A. 109, 19691-19696.
14. Thomas, S., Wright, K. J., Le Corre, S., Micalizzi, A., Romani, M., Abhyankar, A., Saada, J., Perrault, I., Amiel, J., Litzler, J., Filhol, E., Elkhartoufi, N., Kwong, M., Casanova, J. L., Boddaert, N., Baehr, W., Lyonnet, S., Munnich, A., Burglen, L., Chassaing, N., Encha-Ravazi, F., Vekemans, M., Gleeson, J. G., Valente, E. M., Jackson, P. K., Drummond, I. A., Saunier, S., and Attie-Bitach, T. (2014) A Homozygous PDE6D Mutation in Joubert Syndrome Impairs Targeting of Farnesylated INPP5E Protein to the Primary Cilium. Hum Mutat. 35, 137-146.
15. Zhang, H., Li, S., Doan, T., Rieke, F., Detwiler, P. B., Frederick, J. M., and Baehr, W. (2007) Deletion of PrBP/delta Impedes Transport of GRK1 and PDE6 Catalytic Subunits to Photoreceptor Outer Segments. Proc Natl Acad Sci U S A. 104, 8857-8862.
16. Zhang, H., Hanke-Gogokhia, C., Jiang, L., Li, X., Wang, P., Gerstner, C. D., Frederick, J. M., Yang, Z., and Baehr, W. (2015) Mistrafficking of Prenylated Proteins Causes Retinitis Pigmentosa 2. FASEB J. 29, 932-942.
17. Lee, J. J., and Seo, S. (2015) PDE6D Binds to the C-Terminus of RPGR in a Prenylation-Dependent Manner. EMBO Rep. 16, 1581-1582.
18. Watzlich, D., Vetter, I., Gotthardt, K., Miertzschke, M., Chen, Y. X., Wittinghofer, A., and Ismail, S. (2013) The Interplay between RPGR, PDEdelta and Arl2/3 Regulate the Ciliary Targeting of Farnesylated Cargo. EMBO Rep. 14, 465-472.
19. Linari, M., Ueffing, M., Manson, F., Wright, A., Meitinger, T., and Becker, J. (1999) The Retinitis Pigmentosa GTPase Regulator, RPGR, Interacts with the Delta Subunit of Rod Cyclic GMP Phosphodiesterase. Proc Natl Acad Sci U S A. 96, 1315-1320.
20. Rao, K. N., Zhang, W., Li, L., Anand, M., and Khanna, H. (2016) Prenylated Retinal Ciliopathy Protein RPGR Interacts with PDE6delta and Regulates Ciliary Localization of Joubert Syndrome-Associated Protein INPP5E. Hum Mol Genet. 25, 4533-4545.
21. Chandra, A., Grecco, H. E., Pisupati, V., Perera, D., Cassidy, L., Skoulidis, F., Ismail, S. A., Hedberg, C., Hanzal-Bayer, M., Venkitaraman, A. R., Wittinghofer, A., and Bastiaens, P. I. (2011) The GDI-Like Solubilizing Factor PDEdelta Sustains the Spatial Organization and Signalling of Ras Family Proteins. Nat Cell Biol. 14, 148-158.
22. Nancy, V., Callebaut, I., El Marjou, A., and de Gunzburg, J. (2002) The Delta Subunit of Retinal Rod cGMP Phosphodiesterase Regulates the Membrane Association of Ras and Rap GTPases. J Biol Chem. 277, 15076-15084.
23. Marzesco, A. M., Galli, T., Louvard, D., and Zahraoui, A. (1998) The Rod cGMP Phosphodiesterase Delta Subunit Dissociates the Small GTPase Rab13 from Membranes. J Biol Chem. 273, 22340-22345.
|Science Writers||Anne Murray|
|Authors||Zhe Chen, Jianhui Wang, Ryan Solts, Noelle Hutchins, Takuma Misawa, and Bruce Beutler|