Phylogeny, historical biogeography, and character evolution in bumble bees (Bombus: Apidae) based on simultaneous analysis of three nuclear gene sequences.
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Animals↗
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Modeling amino acid substitution patterns in orthologous and paralogous genes.
We study to what degree patterns of amino acid substitution vary between genes using two models of protein-coding gene evolution. The first divides the amino acids into groups, with one substitution rate for pairs of residues in the same group and a second for those in differing groups. Unlike previous applications of this model, the groups themselves are estimated from data by simulated annealing. The second model makes substitution rates a function of the physical and chemical similarity between two residues. Because we model the evolution of coding DNA sequences as opposed to protein sequences, artifacts arising from the differing numbers of nucleotide substitutions required to bring about various amino acid substitutions are avoided. Using 10 alignments of related sequences (five of orthologous genes and five gene families), we do find differences in substitution patterns. We also find that, although patterns of amino acid substitution vary temporally within the history of a gene, variation is not greater in paralogous than in orthologous genes. Improved understanding of such gene-specific variation in substitution patterns may have implications for applications such as sequence alignment and phylogenetic inference.
Actins↗
Altered functionality in rhodopsin point mutants associated with retinitis pigmentosa.
Point mutations found in rhodopsin associated with the retinal degenerative disease retinitis pigmentosa have been expressed in mammalian COS-1 cells, purified, and characterised. The mutations characterised-most of them for the first time-have been Met44Thr, Gly114Asp, Arg135Leu, Val137Met, and Pro171Leu in the transmembrane domain; Leu328Pro and Ala346Pro in the C-terminal tail of the cytoplasmic domain; and Gly106Trp in the intradiscal domain. Several of these mutations cause misfolding which results in impaired 11-cis-retinal binding. Two of them, Met44Thr and Val137Met, show spectral and structural features similar to those of wild type rhodopsin (Type I mutants) but significantly increased transducin initial activation rates. We propose that, in the case of these mutants, abnormal functioning resulting in faster activation kinetics could also play a role in retinitis pigmentosa by altering the stoichiometric balance of the different proteins involved in the phototransduction biochemical reactions.
Amino Acid Sequence↗
Cloning of cDNA and amino acid sequence of one of chicken cone visual pigments.
The chicken has four kinds of color visual pigments, in addition to rhodopsin. A chicken genomic DNA library was screened with cDNA of human red-sensitive pigment and a chicken genomic DNA fragment including rhodopsin exons 2, 3 and 4, and then a genomic DNA fragment encoding a visual pigment, possibly an iodopsin, was cloned. A cDNA library, constructed from chicken retina mRNA, was screened with the genomic DNA fragment and the cDNA of human red-sensitive pigment, and the cDNA encoding the pigment was cloned. The nucleotide sequence of this cDNA was similar to that of the human red-sensitive pigment, with identities of 78% for the nucleotide sequence and 84% for the amino acid sequence with human red-sensitive pigment.
Amino Acid Sequence↗
Light-induced conformational changes in the extradiscal regions of bovine rhodopsin.
Light-induced conformational changes occurring at the cytosolic surface of rhodopsin were investigated by performing limited digestions of native and illuminated visual pigment with thermolysin, Arg-C endoproteinase, papain and proteinase K. A higher susceptibility of the extradiscal regions of the bleached pigment to the proteases were observed together with altered capacities of the digested bleached rhodopsins to activate the cGMP phosphodiesterase. The overall results strongly suggest that light induces conformational changes not only in the C-terminal end but also in the second and the third extradiscal loop of rhodopsin.
3',5'-Cyclic-GMP Phosphodiesterases↗
Monoclonal antibodies to chicken iodopsin.
The protein moiety of chicken iodopsin, R-photopsin, was purified from the chicken retina using a sucrose flotation method followed by two steps of column chromatography. Apparent molecular weights of R-photopsin and scotopsin (the protein moiety of chicken rhodopsin), which was partly purified in the process of purification of R-photopsin, were estimated to be 34,000 and 36,000, respectively, by sodium docecylsulfate-polyacrylamide gel electrophoresis. Using the purified R-photopsin as an antigen, four kinds of hybridoma cells which secreted monoclonal antibodies specific for R-photopsin and iodopsin were prepared. The antibodies thus obtained reacted with neither other chicken cone visual pigments nor rhodopsin as analyzed by immunoblots and immunoprecipitation methods. All the monoclonal antibodies stained the majority of the cone outer segments in chicken retina, while an antiserum raised against cattle rhodopsin stained the rod outer segments as well as some cone outer segments in the retina.
Animals↗
Genetics and evolution of ultraviolet vision in vertebrates.
Various vertebrates use ultraviolet (UV) vision for such basic behaviors as mating, foraging, and predation. We have successfully interchanged the color-sensitivities of the mouse UV pigment and the human blue pigment by introducing forward and reverse mutations at five sites. This unveils for the first time the general mechanism of UV vision. Most contemporary UV pigments in vertebrates have maintained their ancestral functions by accumulating no more than one of the five specific amino acid changes. The avian lineage is an exception, where the ancestral pigment lost UV-sensitivity but some descendants regained it by one amino acid replacement at an entirely different site.
Amino Acid Sequence↗
Regeneration of ultraviolet pigments of vertebrates.
We report here the regeneration of the visual pigments of mouse, rat, goldfish and pigeon, which have wavelengths of maximal absorption at 359 nm, 358 nm, 359 nm, and 393 nm, respectively. The construction and functional assays of the ultraviolet or near-ultraviolet pigments from a wide range of vertebrate species will allow us to study the molecular bases of ultraviolet vision for the first time.
Amino Acid Sequence↗
N-linked glycosylation of Drosophila rhodopsin occurs exclusively in the amino-terminal domain and functions in rhodopsin maturation.
Immature Drosophila rhodopsin is N-glycosylated, but undergoes complete deglycosylation during the process of protein maturation. In order to elucidate the site of glycosylation and its role in rhodopsin synthesis, we investigated the in vitro and in vivo synthesis of rhodopsin whose putative N-glycosylation sites (Asn-20 and Asn-196) were replaced by isoleucine. The results demonstrated that immature rhodopsin binds a single oligosaccharide chain exclusively at Asn-20 in the N-terminal extracellular domain. Furthermore, the results gave the first evidence directly indicating that deletion of the oligosaccharide chain markedly impedes rhodopsin maturation.
Amidohydrolases↗
Correlation of gene structure and psychophysical measurement in red-green color vision deficiency in Chinese.
PURPOSE: To study the correlation of genotype for X-linked red-green gene array with color vision phenotype in 58 subjects with red-green color vision deficiency. METHODS: The molecular structure of red and green pigment genes on 58 X chromosomes was studied exon-by-exon by using heteroduplex-SSCP analysis and sequencing. The color vision of these subjects was determined by a Neitz anomaloscope. RESULTS: Variations in the red and green pigment genes were detected in 43 subjects and a hybrid gene was found in 27 subjects. About 50% of the fusion sites occurred at intron 2-3. All 3 anomalous trichromats with intron 4 fusion were mild type but another 3 with intron 2-3 fusion were severe type. No subjects with mild type of color vision defects had a fusion site at intron 2-3 or its upstream. Three subjects with complete deletion of the green pigment gene manifested deuteranomaly. CONCLUSIONS: Protans can be differentiated from deutans on the basis of genotype. It is still difficult to establish a clear correlation of different anomalous trichromats with genotype. The fusion site of a hybrid gene affects the phenotype to some degree. Intron 2-3 is the common place for gene crossover.
Blotting, Southern↗
Chromatographic resolution of the rod pigment from the four cone pigments of the chicken retina.
Chicken rod and cone pigments are chromatographically resolved using a combination of stepwise elution from a concanavalin A affinity column and a secondary ion exchange purification. The rod pigment rhodopsin and the cone pigment iodopsin are purified to homogeneity. There is a partial separation of three other cone pigments: chicken green, chicken blue, and chicken violet, making clear that this is at least a tetrachromatic cone system.
Animals↗
Severity of color vision defects: electroretinographic (ERG), molecular and behavioral studies.
Earlier research on phenotype/genotype relationships in color vision has shown imperfect predictability of color matching from the photopigment spectral sensitivities inferred from molecular genetic analysis. We previously observed that not all of the genes of the X-chromosome linked photopigment gene locus are expressed in the retina. Since sequence analysis of DNA does not necessarily reveal which of the genes are expressed into photopigments, we used ERG spectral sensitivities and adaptation measurements to assess expressed photopigment complement. Many deuteranomalous subjects had L, M, and L-M hybrid genes. The ERG results showed that M pigment is not present in measurable quantities in deutan subjects. Using these results to determine gene expression improved the correlations between inferred pigment separation and color matching. Furthermore, we found a subject who had normal L and M genes and normal proximal promoter sequences, yet he had a single photopigment (M) by ERG and tested as a protanope. These results demonstrate the utility of ERG measurements in studies of molecular genetics of color vision deficiencies, and further support the conclusion that not all genes are expressed in color deficient subjects. In particular, deuteranomaly requires a presently unknown mechanism of selective expression which excludes normal M genes and allows expression of L-M hybrid genes in one cone type, and the normal L in another.
Adaptation, Ocular↗
Molecular evolution of trichromacy in primates.
Although trichromacy in Old and New World primates is based on three visual pigments with spectral peaks in the violet (SW, shortwave), green (MW, middlewave) and yellow-green (LW, longwave) regions of the spectrum, the underlying genetic mechanisms differ. The SW pigment is encoded in both cases by an autosomal gene and, in Old World primates, the MW and LW pigments by separate genes on the X chromosome. In contrast, there is a single polymorphic X-linked gene in most New World primates with three alleles coding for spectrally distinct pigments. The one reported exception to this rule is the New World howler monkey that follows the Old World system of separate LW and MW genes. A comparison of gene sequences in these different genetic systems indicates that the duplication that gave rise to the separate MW and LW genes of Old World primates is more ancient than that in the howler monkey. In addition, the amino acid sequences of the two howler monkey pigments show similarities to the pigments encoded by the polymorphic gene of other New World primates. It would appear therefore that the howler monkey gene duplication arose after the split between New and Old World primates and was generated by an unequal crossover that placed two different forms of the New World polymorphic gene on to a single chromosome. In contrast, the lack of identity at variable sites within the New and Old World systems argues for the origin of the separate genes in Old World primates by the duplication of a single form of the gene followed by divergence to give spectrally distinct LW and MW pigments. In contrast, the similarity in amino acid variation across the tri-allelic system of New World primates indicates that this polymorphism had a single origin in New World primates. A striking feature of all these pigments is the use of a common set of substitutions at three amino acid sites to achieve the spectral shift from MW at around 530 nm to LW at around 560 nm. The separate origin of the trichromacy in New and Old World primates would indicate that the selection of these three sites is the result of convergent evolution, perhaps as a consequence of visual adaptation in both cases to foraging for yellow and orange fruits against a green foliage.
Alouatta↗
Roles of PACAP-containing retinal ganglion cells in circadian timing.
The brain's biological clock located in the suprachiasmatic nucleus (SCN) generates circadian rhythms in physiology and behavior. The clock-driven rhythms need daily adjustment (entrainment) to be synchronized with the astronomical day of 24 h. The most important stimulus for entrainment of the clock is the light-dark (LD) cycle. In this review functional elements of the light entrainment pathway will be considered with special focus on the neurotransmitter pituitary adenylate cyclase-activating polypeptide (PACAP), which is found exclusively in the monosynaptic neuronal pathway mediating light information to the SCN, the retinohypothalamic tract (RHT). The retinal ganglion cells of the RHT are intrinsically photosensitive due to the expression of melanopsin and seem to constitute a non-image forming photosensitive system in the mammalian eye regulating circadian timing, masking behavior, light-regulated melatonin secretion, and the pupillary light reflex. Evidence from in vitro and in vivo studies and studies of mice lacking PACAP and the specific PACAP receptor (PAC1) indicate that PACAP and glutamate are neurotransmitters in the RHT which in a clock and concentration-dependent manner interact during light entrainment of the clock.
Animals↗
Photoreceptor rescue in the dystrophic retina by transplantation of retinal pigment epithelium.
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Age Factors↗
Analysis of functional microdomains of rhodopsin.
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Amino Acid Sequence↗
Structural determinants of active state conformation of rhodopsin: molecular biophysics approaches.
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Amino Acid Substitution↗