Rhodopsin: Structural Basis of Molecular Physiology

Menon, Santosh T.; Han, May; Sakmar, Thomas P.

doi:10.1152/physrev.2001.81.4.1659

Cited by 297 publications

(309 citation statements)

References 255 publications

(217 reference statements)

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“…The CarO protein belongs to the opsin family and was found to show significant degrees of identity with ops and nop-1 from Leptospaeria maculans and Neurospora crassa, respectively. Opsins are membrane photoreceptors which play an important role in light detection in algae (Ridge 2002) and animals (Menon et al 2001). However, understanding the biological function of these proteins in fungi needs further investigations.…”

Section: Discussionmentioning

confidence: 99%

Tagging target genes of the MAT1-2-1 transcription factor in Fusarium verticillioides (Gibberella fujikuroi MP-A)

Keszthelyi

Jeney

Kerényi

et al. 2006

Antonie van Leeuwenhoek

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Mating type in filamentous ascomycetes is controlled by idiomorphic alleles, named MAT1-1 and MAT1-2, which contain 1-3 genes. Of these genes MAT1-1-1 and MAT1-2-1 encode putative transcription factors and are thus considered to be the major regulators of sexual communication and mating. Fungi with no known sexual stage may also have fully functional mating type genes and therefore it was plausible to hypothesize that the MAT products may also regulate other types of genes not involved directly in the mating process. To identify putative target genes of these transcription factors in Fusarium verticillioides, DMAT1-2-1 knock out mutants were produced and transcript profiles of mutant and wild type were compared by means of differential cDNA hybridization. Clones, either up-or down-regulated in the DMAT1-2-1 mutant were sequenced and a total of 248 sequences were blasted against the NCBI database as well as the Gibberella zeae and Gibberella moniliformis genomes. Fifty-five percent of the clones were down-regulated in the mutant, indicating that the MAT1-2-1 product positively affected these tagged sequences. On the other hand, 45% were found to be up-regulated in the mutant, suggesting that the MAT1-2-1 product also exerted a negative regulatory function on this set of genes. Sequences involved in protein synthesis and metabolism occurred more frequently among the clones up-regulated in the mutant, whereas genes belonging to cell signalling and communication were especially frequently tagged among the sequences down-regulated in the mutant.

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Section: Discussionmentioning

confidence: 99%

Tagging target genes of the MAT1-2-1 transcription factor in Fusarium verticillioides (Gibberella fujikuroi MP-A)

Keszthelyi

Jeney

Kerényi

et al. 2006

Antonie van Leeuwenhoek

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“…Several highly conserved motifs in GPCRs are also present in the MOR42 subfamily, including the (D/E)R(Y/W) motif located near the cytoplasmic end of TMIII and the NPXXY motif in TMVII. These motifs are thought to form a hydrogen bond network important for inter-helical interactions (37) and may play a role in receptor transformation from an inactive form to an active, G protein-coupled conformation (38). Conserved prolines that produce kinks in the helix structure of MOR42-3 are Pro-162 (in TMIV, equivalent to Pro-170 in rhodopsin) and Pro-303 (in TMVII, position 291 in rhodopsin).…”

Section: Initial Mutation Screen Of Mor42-3-mentioning

confidence: 99%

The Molecular Basis for Ligand Specificity in a Mouse Olfactory Receptor

Abaffy

Malhotra

Luetje

2007

Journal of Biological Chemistry

103

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Sequence differences between members of the mouse olfactory receptor MOR42 subfamily (MOR42-3 and MOR42-1) are likely to be the basis for variation in ligand binding preference among these receptors. We investigated the specificity of MOR42-3 for a variety of dicarboxylic acids. We used site-directed mutagenesis, guided by homology modeling and ligand docking studies, to locate functionally important residues. Receptors were expressed in Xenopus oocytes and assayed using high throughput electrophysiology. The importance of the Val-113 residue, located deep within the receptor, was analyzed in the context of interhelical interactions. We also screened additional residues predicted to be involved in ligand binding site, based on comparison of ortholog/paralog pairs from the mouse and human olfactory receptor genomes (Man, O., Gilad, Y., and Lancet, D. (2004) Protein Sci. 13, 240 -254). A network of 8 residues in transmembrane domains III, V, and VI was identified.These residues form part of the ligand binding pocket of MOR42-3. C12 dicarboxylic acid did not activate the receptor in our functional assay, yet our docking simulations predicted its binding site in MOR42-3. Binding without activation implied that C12 dicarboxylic acid might act as an antagonist. In our functional assay, C12 dicarboxylic acid did indeed act as an antagonist of MOR42-3, in agreement with molecular docking studies. Our results demonstrate a powerful approach based on the synergy between computational predictions and physiological assays.

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“…Kozmik et al 2008;Menon et al 2001;Salcedo et al 2003;Yokoyama 1997). In addition, several studies have investigated the molecular basis of the multiple steps in phototransduction, from opsin activation to nervous impulse.…”

Section: Origins Of Variation In Eye Evolutionmentioning

confidence: 99%

Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

Oakley

Pankey

2008

Evo Edu Outreach

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Eyes provide a rich narrative for understanding evolution, having attracted the attention of preeminent scientists and communicators alike. Until recently, this narrative has focused primarily on the evolution of eye structure and far less on biochemistry or genetics. Although eye biochemistry was once likened to an unknown "black box;" the flood of discoveries in biochemistry is now allowing an increasingly detailed understanding of the processes involved in vision. As a result, evolutionary comparative ("tree-thinking") analyses that use these data currently allow a new and still unfolding narrative, both richer in detail and more comprehensive in scope. Rather than toppling evolutionary theory by finding irreducibly complex molecular machines, eye evolution provides detailed accounts of how natural processes tinker with existing genetic components, duplicating and recombining them, to yield complex, intricate, and highly functional eyes. Understanding the new biochemical narrative is critical for researchers and teachers alike, in order to answer antievolutionist claims, and to provide an up-to-date account of the state of knowledge on the subject of eye evolution.Keywords Evolution . Phototransduction . Vision . Eyes . Phylogeny . Novelty . ComplexityThe evolutionary history of eyes is one of the most intriguing and often-told stories in biology. It is a topic researched and discussed by members of the pantheon of evolutionists, including Darwin (1859), Salvini-Plawen and Mayr (1977), Gould (1994), andDawkins (1996). The commonly told story is familiar and has not changed much since Darwin first proposed it: A light-sensitive nerve gradually changes over evolutionary time, adding complexity across the generations. To Darwin's sketch, Salvini-Plawen and Mayr (1977) added detail, and Nilsson and Pelger (1994) tested the temporal component. The ancient canon of gradual evolution is certainly valuable for demonstrating that some assumptions are met for the hypothesis that natural selection generates complexity, serving as a colorful and graphical example (Dawkins 1996). However, this account-if taken too far-can easily be criticized, as demonstrated, for example, by proponents of Intelligent Design (ID; Behe 1996) who point out that the Darwinian canon ignores complexity at the molecular level. The structure of this article is first to briefly present the "gradual morphological" account of the evolution of eye form and to describe how this account relates to understanding evolution by natural selection. Section II will point out two primary limitations of this "gradual morphological" model, including one highlighted by ID proponents. Third, the paper will present molecular and biochemical details describing how phototransduction (the cascade of signaling events that generate a nervous impulse in response to light) and complex lenses evolved. These two case studies provide specific details about how eyes evolved. The processes elucidated, such as duplication and co-option (the use of existing components ...

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Rhodopsin: Structural Basis of Molecular Physiology

Cited by 297 publications

References 255 publications

Tagging target genes of the MAT1-2-1 transcription factor in Fusarium verticillioides (Gibberella fujikuroi MP-A)

Tagging target genes of the MAT1-2-1 transcription factor in Fusarium verticillioides (Gibberella fujikuroi MP-A)

The Molecular Basis for Ligand Specificity in a Mouse Olfactory Receptor

Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

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