Homozygosity Mapping, Gene Structure, and the Mutation Identified in DHDDS
(A) The chromosomal region harboring the homozygous haplotype at chromosome 1 (top). Rulers are based on the February 2009 USCS genome build (hg19). The set of horizontal bars represents the homozygous region in the three different families, as identified by whole-genome SNP analysis. The family number is shown on the left. The region flanked by SNP markers rs3924468 and rs11247703, covering 2.32 Mb between 25.8 and 28.1 Mb on chromosome 1, was considered the shared homozygous region.
(B) Intron-exon structure of DHDDS and known or predicted protein domains. The structure of DHDDS is depicted (top) with exons marked as black rectangles (wider for the coding region). The location of the c.124A>G (p.Lys42Glu) missense mutation is marked below exon 3. Known or putative domains of the DHDDS enzyme are depicted (bottom), with an asterisk pointing to the mutation position.
(C) Sequence chromatograms of part of DHDDS exon 3 of a homozygous mutant and a wild-type individual. The c.124A>G mutation (boxed) changes an AAG codon to GAG (p.Lys42Glu).
(D) An amino acid sequence alignment of DHDDS including position 42 (boxed). The aa types are color-coded: small aa in red, acidic in blue, basic in magenta, and hydroxyl + amine + basic in green.

Ocular Phenotype of Three Siblings Who Are Homozygous for the DHDDS c.124A>G Mutation
(A) Visual field extent (kinetic perimetry with V-4e test target) expressed as a percentage of normal mean and plotted as a function of age in the three siblings of family MOL0884.
(B) Visual fields (V-4e, I-4e test targets) at different ages showing progressive peripheral vision loss.
(C) Visual acuity (expressed in logMAR units) as a function of age in the patients.
(D) Dark-adapted static perimetric profiles across the horizontal meridian with a 500 nm stimulus in the three siblings. Data span a minimum of 1.5 decades in each patient. Based on two-color (500 nm and 650 nm) dark-adapted perimetry, photoreceptor mediation was determined for each test locus at the earliest (blue letters) and latest (red letters) ages studied. The following abbreviations are used: R, rod-mediated; M, mixed rod- and cone-mediated; C, cone-mediated; N, nasal; T, temporal visual field. Gray represents normal limits (mean ± 2 standard deviation). Hashed band is the location of the physiological blind spot.
(E) Photoreceptor layer thickness topography mapped to a pseudocolor scale (shown above normal map) in a normal subject and in the three affected siblings. Insets: near-infrared excited autofluorescence imaging of melanin fluorophore distribution to estimate retinal pigment epithelium (RPE) layer health.

DHDDS Expression in the Human Retina
(A) Hematoxylin-Eosin stained section of a normal human retina, with identification of the different retinal layers. The following abbreviations are used: GCL, ganglion cell layer; IPL, inner plexiform layer; INL, inner nuclear layer; OPL, outer plexiform layer; ONL, outer nuclear layer, containing the photoreceptor nuclei; IS, inner segments of photoreceptors; OS, outer segments of photoreceptors; RPE, retinal pigment epithelium layer.
(B and C) Low-magnification images of anti-DHDDS antibody-labeled (B, in green fluorescence) and control (C, no primary antibody applied) retinal sections. Note prominent labeling of the rod and cone inner segments. Yellow color of the RPE layer is due to autofluorescence of these cells (original magnification 20×). Scale bar represents 100 μm.
(D and E) Higher-magnification images of the photoreceptor-RPE region. Note segmental staining of the ellipsoid (red arrow) and myoid (white arrow) of the rod photoreceptor inner segments (original magnification 40× with digital zoom). Scale bar represents 25 μm. A representative cone inner segment is marked by a yellow star.

Cosegregation of Mutation and Phenotype in Identified Families
The family number is indicated above the corresponding family tree. Filled symbols represent affected individuals, whereas clear symbols represent unaffected individuals. Generation numbers are depicted on the left. The DHDDS genotype is shown below recruited individual symbols: M/M denotes homozygous for the mutation; M/+ denotes heterozygous for the mutation; +/+ denotes homozygous for the wild-type allele.

DHDDS Transcripts and RT-PCR Analysis in Human Tissues
(A) DHDDS can produce different transcripts through alternative splicing. The scheme represents the full-length open reading frame (ORF) of DHDDS (top), as well as alternatively spliced transcripts identified in this study: skipping of exon 6 (middle) and recognition of a cryptic acceptor site within intron 3 (bottom, blue box), leading to the addition of 23 nucleotides. Arrows represent the location and direction of primers used for RT-PCR (see also Table S3). The NAGNAG sequence in exon 9 represents an alternative usage of either the first or second NAG sequence as an acceptor splice site of intron 8. Ex denotes exon, Int denotes intron, PTC denotes premature termination codon. It should be noted that a transcript in which exon 5 is skipped has been deposited in GenBank, but we were not able to verify it in any of the analyzed tissues.
(B) The expression level of DHDDS in 21 tissues is depicted. Two sets of primers were used to amplify DHDDS: set 1 amplified exons 4 trough 6 (F4-R6), and set 2 primers amplified exons 5 through 7 (F5-R7). PGM1 amplification served as a control for cDNA amount used in the PCR reaction (set 3). The lower faint band in set 2 could be observed in all tissues, and sequence analysis revealed skipping of exon 6.

The Function of the DHDDS Enzyme and Possible Mechanisms Underlying DHDDS-Related Retinal Degeneration
(A) DHDDS is a key enzyme in dolichol biosynthesis, which catalyzes cis-prenyl chain elongation to produce the polyprenyl backbone of dolichol. It is required for two enzymatic steps (arrows) along the dolichol pathway.
(B) Schematic representation of the role of dolichol in N-glycosylation. Dolichol is a membrane-bound glycosyl carrier and plays an important role in the biosynthesis of the N-linked oligosaccharide chains of glycoproteins. The two arrows represent multiple steps that are not shown here. N-glycosylation of the opsin molecule is schematically represented on the right. The ribosome (oval shape) synthesizes fresh opsin molecules with two sites of N-glycosylation (ASN) at the N terminus (positions 2 and 15). Dol-PP transfers the oligosaccharide chain to these sites to glycosylate the opsin molecule (based on 49 ).
(C) Scheme of putative mechanisms by which the DHDDS mutation could lead to retinal degeneration. In the top panel, the possibility that the mutation causes a hyperactivity in the enzymatic function of DHDDS leading to excessive accumulation of Dol-P and/or Dol-PP, because of “overflow” of the N-glycosylation pathway, is shown. These substances might be toxic to the photoreceptor cell, causing photoreceptor degeneration. Alternatively, the mutation can by hypormorph, leading to reduced enzymatic function of DHDDS. This might in turn reduce N-glycosylation levels, producing a certain amount of nonglycosylated, and therefore nonfunctional, opsin molecules, leading to photoreceptor degeneration. Either of the proposed two mechanisms might mimic the retinal degeneration phenotype cause by the inhibitor of N-glycosylation followed by exposure to tunicamycin (panel B).