Search

The review discusses the prospects of using rhodopsin as an optogenetic tool for prosthetics of degenerative (blind) eye retina and the principles of optogenetic techniques. Retinal-containing proteins that depolarize/hyperpolarize the plasma membrane of nerve cells and, accordingly, excite/inhibit physiological activity of neurons, are described. The problem of what cells of the degenerative retina can be treated with what particular rhodopsins is discussed in detail. Viruses and promoters required for the rhodopsin gene delivery into the degenerative retina cells are described. In conclusion, main concepts and tasks associated with the optogenetic prosthetic treatment of degenerative retina employing rhodopsins are presented.

Most vertebrates have duplex retinas, with two classes of photoreceptors, rods and cones. In the group of Snakes, however, distinct patterns of retinal morphology are associated with transitions between diurnal-nocturnal habits and reflect important adaptations of their visual system. Pure-cone, pure-rod and duplex retinas were described in different species, and this variability led Gordon Walls (1934) to formulate the transmutation theory, which suggests that rods and cones are not fixed entities, but can assume transitional states. Three opsin genes are expressed in retinas of most snake species, lws, rh1, and sws1, and recent studies have shown that the rhodopsin gene, rh1, is expressed in pure-cone retinas of diurnal snakes. This expression raised many questions about the nature of transmutation and functional aspects of the rhodopsin in a cone-like photoreceptor. Extreme differences in the retinal architecture of diurnal and nocturnal snakes also highlight the complexity of adaptations of their visual structures, which might have contributed to the adaptive radiation of this group and will be discussed in this review.

Summary The presence of exotic fish species in the Baltic Sea and its tributaries poses a serious threat for native ichthyofauna, mainly due to the spread of new pathogens. As the accurate identification of species is essential for an effective assessment of changes related to the appearance of non-native species in an aquatic environment, in this paper we tested the usefulness of biometrics and molecular markers in identifying a specimen from the Mugilidae family found in the Odra estuary. The results demonstrated that unambiguous identification of the specimen using biometric features was impossible due to high morphological similarities shared by grey mullets. Unambiguous identification was possible only due to molecular markers, e.g. rhodopsin gene, which helped to identify the collected fish specimen as Liza ramada (Risso, 1827), the first specimen of this species found in the Odra River estuary. The presence of an L. ramada specimen in the Odra River – which could signal the expansion of non-native species into wider ranges – may be linked to climate change or human activity.

Indirana salelkari, a new species of leaping frog, is described from Netravali, Goa, India. The species can be distinguished from its congeners by a combination of morphological characters, viz., head longer than wide, narrow and deep buccal cavity, vomerine teeth large and acutely placed close to each other, oval choanae, distinct canthus rostralis, first finger longer than or equal to second, presence of double outer palmer tubercles, elongated inner metatarsal tubercle, moderate webbing, discs of fingers and toes with crescentic deep marginal grooves restricted only to the anterior side of the discs, dorsal skin with glandular folds but without warts, ventral skin granular with some mottling on throat and, palms and soles dark brown. Indirana salelkari differs from its sister taxa, I. chiravasi, in the placement and structure of vomerine teeth and choanae. The new species is genetically distinct from I. chiravasi, with a genetic distance of 3.8% for the 16S rRNA gene. We also provide phylogentic placement of Indirana salelkari based on mitochondrial 12S and 16S ribosomal genes and nuclear rhodopsin gene along with molecular clock analysis, which further confirms its genetic distinctness from other related taxa.

Rhodopsin 7 ( Rh7), a new invertebrate Rhodopsin gene, was discovered in the genome of Drosophila melanogaster in 2000, but its function has remained elusive. We generated an Rh7 null mutant ( Rh70) by P element–mediated mutagenesis and found that an absence of Rh7 had significant effects on fly activity patterns during light-dark (LD) cycles: Rh70mutants exhibited less morning activity and a longer siesta than wild-type controls. Consistent with these results, we found that Rh7 appears to be expressed in a few dorsal clock neurons that have been previously implicated in the control of the siesta. We also found putative Rh7 expression in R8 photoreceptor cells of the compound eyes and in the Hofbauer-Buchner eyelets, which have been shown to control the precise timing of locomotor activity. The absence of Rh7 alone impaired neither the flies’ responses to constant white light nor the ability to follow phase shifts of white LD cycles. However, in blue light (470 nm), Rh70mutants needed significantly longer to synchronize than wild-type controls, suggesting that Rh7 is a blue light–sensitive photopigment with a minor contribution to circadian clock synchronization. In combination with mutants that lacked additionally cryptochrome-based and/or eye-based light input to the circadian clock, the absence of Rh7 provoked slightly stronger effects.

Purpose: Autosomal dominant retinitis pigmentosa (adRP) is characterized by an extensive genetic heterogeneity, implicating 27 genes, which account for 50 to 70% of cases. Here 86 Belgian probands with possible adRP underwent genetic testing to unravel the molecular basis and to assess the contribution of the genes underlying their condition. Methods: Mutation detection methods evolved over the past ten years, including mutation specific methods (APEX chip analysis), linkage analysis, gene panel analysis (Sanger sequencing, targeted next-generation sequencing or whole exome sequencing), high-resolution copy number screening (customized microarray-based comparative genomic hybridization). Identified variants were classified following American College of Medical Genetics and Genomics (ACMG) recommendations. Results: Molecular genetic screening revealed mutations in 48/86 cases (56%). In total, 17 novel pathogenic mutations were identified: four missense mutations in RHO, five frameshift mutations in RP1, six mutations in genes encoding spliceosome components (SNRNP200, PRPF8, and PRPF31), one frameshift mutation in PRPH2, and one frameshift mutation in TOPORS. The proportion of RHO mutations in our cohort (14%) is higher than reported in a French adRP population (10.3%), but lower than reported elsewhere (16.5±30%). The prevalence of RP1 mutations (10.5%) is comparable to other populations (3.5%-10%). The mutation frequency in genes encoding splicing factors is unexpectedly high (altogether 19.8%), with PRPF31 the second most prevalent mutated gene (10.5%). PRPH2 mutations were found in 4.7% of the Belgian cohort. Two families (2.3%) have the recurrent NR2E3 mutation p.(Gly56Arg). The prevalence of the recurrent PROM1 mutation p.(Arg373Cys) was higher than anticipated (3.5%). Conclusions: Overall, we identified mutations in 48 of 86 Belgian adRP cases (56%), with the highest prevalence in RHO (14%), RP1 (10.5%) and PRPF31 (10.5%). Finally, we expanded the molecular spectrum of PRPH2, PRPF8, RHO, RP1, SNRNP200, and TOPORS-Associated adRP by the identification of 17 novel mutations, SCOPUS: ar.j, info:eu-repo/semantics/published

Autosomal dominant retinitis pigmentosa (adRP) may be caused by point mutations in the rhodopsin gene in up to 20% of Spanish families. Most of the rhodopsin mutations causing adRP have been reported in the heterozygous state. We describe a patient with adRP who is homozygous for a missense mutation at codon 188 in the second intradiscal domain of rhodopsin. All her sons are heterozygous for the mutation and show an RP phenotype suggesting complete penetrance for this mutation. The homozygous carrier of the mutation Gly-188-Arg in the rhodopsin gene showed a later subjective onset of symptoms than the heterozygotes, suggesting that the photoreceptor degeneration induced by the mutation is not dramatically influenced by mutant allele dosage.

A Spanish family affected with autosomal dominant retinitis pigmentosa (ADRP) with a diffuse phenotype showed a mutation in the rhodopsin gene. The mutation was the transition T?C in codon 186, which has been reported once before in an American patient (Dryja et al., Proc Natl Acad Sci USA 1991;88:9370-9374). This change replaces a serine by a proline in the second intradiscal loop of the protein, generating a molecule that is probably folding- and transport-defective.

More than 100 mutations within the rhodopsin gene have been found to be responsible for some forms of retinitis pigmentosa, a progressive retinal degeneration characterized by night blindness and subsequent disturbance of day vision that may eventually result in total blindness. Congenital stationary night blindness (CSNB) is an uncommon inherited retinal dysfunction in which patients complain of night vision difficulties of a nonprogressive nature only and in which generally there is no involvement of day vision. We report the results of molecular genetic analysis of an Irish family segregating an autosomal dominant form of CSNB in which a previously unreported threonine-to-isoleucine substitution at codon 94 in the rhodopsin gene was found to segregate with the disease. Computer modeling suggests that constitutive activation of transducin by the altered rhodopsin protein may be a mechanism for disease causation in this family. Only two mutations within the rhodopsin gene have been previously reported in patients with congenital stationary night blindness, constitutive activation also having been proposed as a possible disease mechanism.

We have explored the application of triplex technology to the human rhodopsin gene, which encodes a G-protein-linked receptor involved in the genetic disorder autosomal dominant retinitis pigmentosa (ADRP). Our results support the hypothesis that most human genes contain high-affinity triplex sites and further refine the rules governing identification and successful targeting of triplex-forming oligonucleotides (TFOs) to these sites. Using a computer search for sites 15 nucleotides in length and greater than 80% purine, we found 143 distinct sites in the rhodopsin gene and comparable numbers of sites in several other human genes. By applying more stringent criteria, we selected 17 potential target sites in the rhodopsin gene, screened them with a plasmid binding assay, and found 8 that bound TFOs with submicromolar affinity (Kd = 10(-)9-10(-)7 M). We compared purine (GA) and mixed (GT) TFOs at each site, and found that GA-TFOs consistently bound with higher affinity, and were less sensitive to pyrimidine interruptions in the target strand. High G-content favored high-affinity binding; only sites with54% G-content bound TFOs with Kd/= 10(-)8 M.

Mutations in the rhodopsin gene were studied in 23 unrelated Spanish patients with sporadic retinitis pigmentosa (RP). A codon 160 Thr C→A transition was found in 4 of the 23 patients vs. none of the 159 controls (p < 0.001) suggesting that this mutation may be an informative marker in RP.

The Drosophila genetic system has been exploited to identify and analyze many genes that are responsible for the specialized cellular processes and biochemical mechanisms of the photoreceptor cell. The results establish that disruption of many different cellular processes can trigger retinal degeneration. The rhodopsin gene family provides an example in which mutations are known to trigger retinal degeneration in both vertebrates and invertebrates. The Drosophila research has established that dominant rhodopsin mutations disrupt the protein maturation process. This review emphasizes the unique and powerful experimental approaches of Drosophila that are being applied towards understanding the many causes of retinal degeneration.

Wavelet decomposition is applied to the analysis of the nucleotide sequence of the rhodopsin gene of Chinese Hamster cells. The Lipschitz-Holder exponents for the probability measurements of adenine, guanine, thymine and cytosine distributions are obtained. The local scaling found by means of wavelet analysis is argued to be an indication of long-range correlations.

Frequencies of polymorphisms in the rhodopsin gene of Japanese retinitis pigmentosa and normal individuals

Photochemical reaction centers and rhodopsins are the only phototrophic mechanisms known to have evolved on Earth. The minimal cost of bearing a rhodopsin-based phototrophic mechanism in comparison to maintaining a photochemical reaction center suggests that rhodopsin is the more abundant of the two. We tested this hypothesis by conducting a global abundance calculation of phototrophic mechanisms from 116 marine and terrestrial microbial metagenomes. On average, 48% of the cells from which these metagenomes were generated harbored a rhodopsin gene, exceeding the reaction center abundance by threefold. Evidence from metatranscriptomic data suggests that this genomic potential is realized to a substantial extent, at least for the small-sized (>0.8 μm) of microbial fractions.

To describe early-onset cystoid macular edema (CME) in a family with retinitis pigmentosa (RP) due to the p.P347L in the rhodopsin gene (RHO).All affected family members, including a 44-year-old mother and four children in their teens (two daughters, 17 and 15 years old, and two sons, 13 and 11 years old), have a mutation of p.P347L in RHO. Funduscopy, Goldmann perimetry, spectral domain optical coherence tomography (SD-OCT) and electroretinogram (ERG) were performed in all affected members to assess the retinal anatomy and function.The mother had very poor visual acuity of light perception in both eyes, and marked foveal atrophy was observed via SD-OCT. Although the macular appearance in the funduscopy looked unremarkable in the four children, SD-OCT revealed bilateral CME in all the children. The rod response in ERG was extinguished and the cone response was decreased in all children.The results present the possibility that CME in RP patients may be associated with a specific genotype such as the p.P347L in RHO. We speculate that the severe visual prognosis of this mutation may be related to early-onset CME, as shown in this family. However, further investigation in more RP patients with this mutation and CME will be needed.

In light of the elucidation of the molecular pathogenesis of some dominantly inherited retinal degenerations over the past two decades, it is timely to explore possible means of therapeutic intervention for such diseases. However, the presence of significant levels of intergenic and intragenic genetic heterogeneity in this group of dominant conditions represents a barrier to the development of therapies focused on correcting the primary genetic defect. More than 60 genes have been implicated in dominant retinopathies and indeed over 150 different mutations in the rhodopsin gene alone have been identified in patients with autosomal dominant retinitis pigmentosa. Employing next-generation sequencing to characterise populations of retinal degeneration patients genetically over the coming years will beyond doubt serve to highlight further the immense genetic heterogeneity inherent in this group of disorders. Such diversity in genetic aetiologies has promoted the search for therapeutic solutions for dominantly inherited retinopathies that are independent of disease-causing mutations. The various approaches being considered to provide mutation-independent therapies for these dominant conditions will be discussed in the review, as will the preclinical data supporting the further development of such strategies.

Fractal dimension and Shannon entropy were used to analyze the nucleotide fluctuation of dim-light vision rhodopsin gene. The maximal absorption wavelengths of the studied gene sequences span a range of 480 nm to 526 nm. The di-nucleotide Shannon entropy correlates with (a) the mono-nucleotide Shannon entropy with R² of 0.99; (b) the CG+GC content with R² of 0.86 (N = 6). The absorption maximal wavelength correlation with the CG+GC content was found to have an R² of 0.82 for the gene sequence and 0.91 for the mRNA sequence. The fractal dimensions of the gene sequences and mRNA sequences were found to be correlated with R² of 0.78. Selection pressure on the CG+GC content at the gene and mRNA levels would be a consistent observation for phenotype dim-light functionality.