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https://www.readbyqxmd.com/read/29143302/convergent-selection-pressures-drive-the-evolution-of-rhodopsin-kinetics-at-high-altitudes-via-non-parallel-mechanisms
#1
Gianni M Castiglione, Ryan K Schott, Frances E Hauser, Belinda S W Chang
Convergent evolution in response to similar selective pressures is a well-known phenomenon in evolutionary biology. Less well understood is how selection drives convergence in protein function, and the underlying mechanisms by which this can be achieved. Here we investigate functional convergence in the visual system of two distantly related lineages of high-altitude adapted Andean and Himalayan catfishes. Statistical analyses revealed in the two high-altitude lineages, a parallel acceleration of evolutionary rates in rhodopsin, the dim-light visual pigment...
November 16, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29138475/the-rises-and-falls-of-opsin-genes-in-59-ray-finned-fish-genomes-and-their-implications-for-environmental-adaptation
#2
Jinn-Jy Lin, Feng-Yu Wang, Wen-Hsiung Li, Tzi-Yuan Wang
We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29134709/light-sensing-by-opsins-and-fungal-ecology-nop-1-modulates-entry-into-sexual-reproduction-in-response-to-environmental-cues
#3
Zheng Wang, Junrui Wang, Ning Li, Jigang Li, Frances Trail, Jay C Dunlap, Jeffrey P Townsend
Understanding the genetic basis of the switch from asexual to sexual lifestyles in response to sometimes rapid environmental changes is one of the major challenges in fungal ecology. Light appears to play a critical role in the switch-but fungal genomes harbor diverse light sensors. Fungal opsins are homologous to bacterial green-light sensory rhodopsins, and their organismal functions in fungi have not been well understood. Three of these opsin-like proteins were widely distributed across fungal genomes, but homologs of the Fusarium opsin-like protein CarO were present only in plant-associated fungi...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29123501/gonadotropin-releasing-hormone-gnrh-receptor-structure-and-gnrh-binding
#4
REVIEW
Colleen A Flanagan, Ashmeetha Manilall
Gonadotropin-releasing hormone (GnRH) regulates reproduction. The human GnRH receptor lacks a cytoplasmic carboxy-terminal tail but has amino acid sequence motifs characteristic of rhodopsin-like, class A, G protein-coupled receptors (GPCRs). This review will consider how recent descriptions of X-ray crystallographic structures of GPCRs in inactive and active conformations may contribute to understanding GnRH receptor structure, mechanism of activation and ligand binding. The structures confirmed that ligands bind to variable extracellular surfaces, whereas the seven membrane-spanning α-helices convey the activation signal to the cytoplasmic receptor surface, which binds and activates heterotrimeric G proteins...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29122605/phenotypic-characterization-of-p23h-and-s334ter-rhodopsin-transgenic-rat-models-of-inherited-retinal-degeneration
#5
Matthew M LaVail, Shimpei Nishikawa, Roy H Steinberg, Muna I Naash, Jacque L Duncan, Nikolaus Trautmann, Michael T Matthes, Douglas Yasumura, Cathy Lau-Villacorta, Jeannie Chen, Ward M Peterson, Haidong Yang, John G Flannery
We produced 8 lines of transgenic (Tg) rats expressing one of two different rhodopsin mutations in albino Sprague-Dawley (SD) rats. Three lines were generated with a proline to histidine substitution at codon 23 (P23H), the most common autosomal dominant form of retinitis pigmentosa in the United States. Five lines were generated with a termination codon at position 334 (S334ter), resulting in a C-terminal truncated opsin protein lacking the last 15 amino acid residues and containing all of the phosphorylation sites involved in rhodopsin deactivation, as well as the terminal QVAPA residues important for rhodopsin deactivation and trafficking...
November 6, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/29118188/structure-and-monomer-dimer-equilibrium-for-the-guanylyl-cyclase-domain-of-the-optogenetics-protein-rhogc
#6
Ramasamy P Kumar, Benjamin R Morehouse, Josiane Fofana, Melissa M Trieu, Daniel H Zhou, Molly O Lorenz, Daniel D Oprian
RhoGC is a fusion protein from the aquatic fungus Blastocladiella emersonii, combining a type I rhodopsin domain with a guanylyl cyclase domain. It has generated excitement as an optogenetics tool for the manipulation of cyclic nucleotide signaling pathways. To investigate the regulation of the cyclase activity, we isolated the guanylyl cyclase domain from Escherichia coli with (GCwCCRho) and without (GCRho) the coiled-coil (CC) linker. Both constructs were constitutively active but were monomeric as determined by size-exclusion chromatography and analytical ultracentrifugation, whereas other class III nucleotidyl cyclases are functional dimers...
November 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29117518/protein-sequence-and-membrane-lipid-roles-in-the-activation-kinetics-of-bovine-and-human-rhodopsins
#7
Istvan Szundi, Chie Funatogawa, Ying Guo, Elsa C Y Yan, David S Kliger
Rhodopsin is a G protein-coupled receptor found in the rod outer segments in the retina, which triggers a visual response under dim light conditions. Recently, a study of the late, microsecond-to-millisecond kinetics of photointermediates of the human and bovine rhodopsins in their native membranes revealed a complex, double-square mechanism of rhodopsin activation. In this kinetic scheme, the human rhodopsin exhibited more Schiff base deprotonation than bovine rhodopsin, which could arise from the ∼7% sequence difference between the two proteins, or from the difference between their membrane lipid environments...
November 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29116474/comparative-transcriptomes-and-reciprocal-best-hit-analysis-revealed-potential-pigment-genes-in-two-color-forms-of-tetranychus-urticae
#8
Yi-Dan Mo, Si-Xia Yang, Jing-Yu Zhao, Peng-Yu Jin, Xiao-Yue Hong
Tetranychus urticae Koch is a worldwide agricultural pest. There are two color forms: red and green. The molecular mechanism underlying this color variation is unknown. To elucidate the mechanism, we characterized differentially expressed pigment pathway genes shared in the transcriptomes of these two forms using RNA sequencing and reciprocal best hit analysis. Differentially expressed pigment pathway genes were determined by qRT-PCR to confirm the accuracy of RNA-Seq. The transcriptomes revealed 963 differentially expressed genes (DEGs), of which 687 DEGs were higher in the green form...
November 7, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/29112449/an-average-solvent-electrostatic-configuration-protocol-for-qm-mm-free-energy-optimization-implementation-and-application-to-rhodopsin-systems
#9
Yoelvis Orozco-Gonzalez, Madushanka Manathunga, María Del Carmen Marín, Damianos Agathangelou, Kwang-Hwan Jung, Federico Melaccio, Nicolas Ferré, Stefan Haacke, Kaline Coutinho, Sylvio Canuto, Massimo Olivucci
A novel atomistic methodology to perform free energy geometry optimization of a retinal chromophore covalently bound to any rhodopsin-like protein cavity is presented and benchmarked by computing the absorption maxima wavelengths (λmax) of distant rhodopsin systems. The optimization is achieved by computing the Nagaoka's Free Energy Gradient (FEG) within an Average Solvent Electrostatic Configuration (ASEC) atomistic representation of the thermodynamic equilibrium and minimizing such quantity via an iterative procedure based on sequential classical MD and constrained QM/MM geometry optimization steps...
November 7, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29111831/comparison-of-different-cell-culture-media-in-the-model-of-the-isolated-and-superfused-bovine-retina-investigating-the-limits-of-more-physiological-perfusion-solutions
#10
José Hurst, Milda Vitkute, Kathleen Hofmann, Sebastian Müller, Marina Löscher, Karl-Ulrich Bartz-Schmidt, Martin S Spitzer, Sven Schnichels, Kai Januschowski
PURPOSE: The isolated superfused retina is a standardized tool in ophthalmological research. However, stable electroretinogram (ERG) responses can only be obtained for around eight hours; therefore, limiting its use. The aim of this study was to evaluate the short-term potential of different cell culture media and to promote long-term testing based on the results obtained. MATERIALS AND METHODS: For the experimental procedure bovine retinae were prepared and perfused with the standard Sickel solution and an ERG was performed...
November 7, 2017: Current Eye Research
https://www.readbyqxmd.com/read/29111729/retinal-binding-to-apo-gloeobacter-rhodopsin-the-role-of-ph-and-retinal-carotenoid-interaction
#11
Sankar Jana, Tamar Eliash, Kwang-Hwan Jung, Mordechai Sheves
Over the last few decades, the structure, functions, properties and molecular mechanisms of retinal proteins have been studied extensively. The newly studied retinal protein Gloeobacter rhodopsin (gR) acts as a light-driven proton pump, transferring a proton from the cytoplasmic region to the extracellular region of a cell following light absorption. It was previously shown that gR can bind the carotenoid salinixanthin (sal). In the present study, we report the effect of pH on the binding of retinal to the apo-protein of gR, in the presence and absence of sal, to form the gR pigment...
November 7, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29100828/conditional-loss-of-spata7-in-photoreceptors-causes-progressive-retinal-degeneration-in-mice
#12
Aiden Eblimit, Smriti Akshay Agrawal, Kandace Thomas, Ivan Assenov Anastassov, Tajiguli Abulikemu, Graeme Mardon, Rui Chen
The mammalian retina consists of multiple cell layers including photoreceptor cells, which are light sensing neurons that play essential functions in the visual process. Previously, we identified mutations in SPATA7, encoding spermatogenesis associated protein 7, in families with Leber Congenital Amaurosis (LCA) and juvenile Retinitis Pigmentosa (RP), and showed that Spata7 null mice recapitulate the human disease phenotype of retinal degeneration. SPATA7 is expressed in the connecting cilium of photoreceptor (PR) cells in the mouse retina, as well as in retinal pigment epithelium (RPE) cells, but the functional role of Spata7 in the RPE remains unknown...
October 31, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/29083892/theory-and-simulation-of-the-ultrafast-double-bond-isomerization-of-biological-chromophores
#13
Samer Gozem, Hoi Ling Luk, Igor Schapiro, Massimo Olivucci
Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field...
October 30, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/29082080/examination-of-drosophila-eye-development-with-third-harmonic-generation-microscopy
#14
Abiramy Karunendiran, Richard Cisek, Danielle Tokarz, Virginijus Barzda, Bryan A Stewart
Third harmonic generation (THG) microscopy can exploit endogenous harmonophores such as pigment macromolecules for enhanced image contrast, and therefore can be used without exogenous contrast agents. Previous studies have established that carotenoid compounds are ideal harmonophores for THG microscopy; we therefore sought to determine whether THG from endogenous carotenoid-derived compounds, such as retinal in photoreceptor cells, could serve as a new label-free method for developmental studies. Here we study the development of the pupal eye in Drosophila melanogaster and determine the localization of rhodopsin using THG microscopy technique...
October 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/29079621/genomes-of-novel-microbial-lineages-assembled-from-the-sub-ice-waters-of-lake-baikal
#15
Pedro J Cabello-Yeves, Tamara I Zemskaya, Riccardo Rosselli, Felipe H Coutinho, Alexandra S Zakharenko, Vadim V Blinov, Francisco Rodriguez-Valera
We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March have been deep sequenced and the reads assembled to generate metagenome assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia Other groups such as Actinobacteria or Proteobacteria were in similar proportions as those found in other lakes...
October 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29078348/bacteriorhodopsin-like-channelrhodopsins-alternative-mechanism-for-control-of-cation-conductance
#16
Oleg A Sineshchekov, Elena G Govorunova, Hai Li, John L Spudich
The recently discovered cation-conducting channelrhodopsins in cryptophyte algae are far more homologous to haloarchaeal rhodopsins, in particular the proton pump bacteriorhodopsin (BR), than to earlier known channelrhodopsins. They uniquely retain the two carboxylate residues that define the vectorial proton path in BR in which Asp-85 and Asp-96 serve as acceptor and donor, respectively, of the photoactive site Schiff base (SB) proton. Here we analyze laser flash-induced photocurrents and photochemical conversions in Guillardia theta cation channelrhodopsin 2 (GtCCR2) and its mutants...
October 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29075762/temporal-properties-of-flicker-ergs-in-rabbit-model-of-retinitis-pigmentosa
#17
Satoshi Okado, Shinji Ueno, Taro Kominami, Ayami Nakanishi, Daiki Inooka, Akira Sayo, Mineo Kondo, Hiroko Terasaki
Purpose: We determined the effects of a remodeled inner retina on the flicker electroretinograms (ERGs) in a rabbit eye at an advanced stage of inherited retinal degeneration. Methods: Six wild-type (WT) and four rhodopsin P347L transgenic (Tg) rabbits were studied at 18 months of age. Flicker ERGs were elicited by sinusoidal stimuli at frequencies of 3.906 to 50.781 Hz. To block the ON and OFF retinal pathways, 2-amino-4-phosphonobutyric acid (APB), and 6-cyano-7-nitroquinoxaline-2, 3(1H, 4H)-dione (CNQX), respectively, were injected intravitreally...
October 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29075512/rhodopsin-gene-copies-in-japanese-eel-originated-in-a-teleost-specific-genome-duplication
#18
Yoji Nakamura, Motoshige Yasuike, Miyuki Mekuchi, Yuki Iwasaki, Nobuhiko Ojima, Atushi Fujiwara, Seinen Chow, Kenji Saitoh
BACKGROUND: Gene duplication is considered important to increasing the genetic diversity in animals. In fish, visual pigment genes are often independently duplicated, and the evolutionary significance of such duplications has long been of interest. Eels have two rhodopsin genes (rho), one of which (freshwater type, fw-rho) functions in freshwater and the other (deep-sea type, ds-rho) in marine environments. Hence, switching of rho expression in retinal cells is tightly linked with eels' unique life cycle, in which they migrate from rivers or lakes to the sea...
2017: Zoological Letters
https://www.readbyqxmd.com/read/29064077/hsp27-immunization-reinforces-aii-amacrine-cell-and-synapse-damage-induced-by-s100-in-an-autoimmune-glaucoma-model
#19
Sabrina Reinehr, Sandra Kuehn, Christina Casola, Dennis Koch, Gesa Stute, Pia Grotegut, H Burkhard Dick, Stephanie C Joachim
Previous studies have revealed a loss of retinal ganglion cells (RGCs) and optic nerve fibers after immunization with the S100B protein. Addition of heat shock protein 27 (HSP27) also leads to a decrease of RGCs. Our present aim has been to analyze various retinal cell types after immunization with S100B or S100B + HSP27 (S100 + HSP). After 28 days, retinas were processed for immunohistology and Western blot. RGCs, immunostained for NeuN, were significantly decreased in the S100 and the S100 + HSP groups...
October 24, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/29063275/intracellular-trafficking-of-gonadotropin-receptors-in-health-and-disease
#20
Alfredo Ulloa-Aguirre, Teresa Zariñán, Rubén Gutiérrez-Sagal, James A Dias
Gonadotropin receptors belong to the highly conserved subfamily of the G protein-coupled receptor (GPCR) superfamily, the so-called Rhodopsin-like family (class A), which is the largest class of GPCRs and currently a major drug target. Both the follicle-stimulating hormone receptor (FSHR) and the luteinizing hormone/chorionic gonadotropin hormone receptor (LHCGR) are mainly located in the gonads where they play key functions associated to essential reproductive functions. As any other protein, gonadotropin receptors must be properly folded into a mature tertiary conformation compatible with quaternary assembly and endoplasmic reticulum export to the cell surface plasma membrane...
September 27, 2017: Handbook of Experimental Pharmacology
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