scholarly journals Determinants shaping the nanoscale architecture of the mouse rod outer segment

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Matthias Pöge ◽  
Julia Mahamid ◽  
Sanae S Imanishi ◽  
Jürgen M Plitzko ◽  
Krzysztof Palczewski ◽  
...  
Keyword(s):  
Outer Segment ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Structural Basis ◽  
Radius Of Curvature ◽  
Rod Photoreceptor ◽  
Molecular Architecture ◽  
Structural Determinants ◽  
Rod Outer Segment ◽  
Wide Range

The unique membrane organization of the rod outer segment (ROS), the specialized sensory cilium of rod photoreceptor cells, provides the foundation for phototransduction, the initial step in vision. ROS architecture is characterized by a stack of identically shaped and tightly packed membrane disks loaded with the visual receptor rhodopsin. A wide range of genetic aberrations have been reported to compromise ROS ultrastructure, impairing photoreceptor viability and function. Yet, the structural basis giving rise to the remarkably precise arrangement of ROS membrane stacks and the molecular mechanisms underlying genetically inherited diseases remain elusive. Here, cryo-electron tomography (cryo-ET) performed on native ROS at molecular resolution provides insights into key structural determinants of ROS membrane architecture. Our data confirm the existence of two previously observed molecular connectors/spacers which likely contribute to the nanometer-scale precise stacking of the ROS disks. We further provide evidence that the extreme radius of curvature at the disk rims is enforced by a continuous supramolecular assembly composed of peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) oligomers. We suggest that together these molecular assemblies constitute the structural basis of the highly specialized ROS functional architecture. Our Cryo-ET data provide novel quantitative and structural information on the molecular architecture in ROS and substantiate previous results on proposed mechanisms underlying pathologies of certain PRPH2 mutations leading to blindness.

scholarly journals Determinants shaping the nanoscale architecture of the mouse rod outer segment

2021 ◽  
Author(s):  
Matthias Pöge ◽  
Julia Mahamid ◽  
Sanae S Imanishi ◽  
Jürgen M Plitzko ◽  
Krzysztof Palczewski ◽  
...  
Keyword(s):  
Outer Segment ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Structural Basis ◽  
Radius Of Curvature ◽  
Rod Photoreceptor ◽  
Molecular Architecture ◽  
Structural Determinants ◽  
Rod Outer Segment ◽  
Wide Range

The unique membrane organization of the rod outer segment (ROS), the specialized sensory cilium of rod photoreceptor cells, provides the foundation for phototransduction, the initial step in vision. ROS architecture is characterized by a stack of identically shaped and tightly packed membrane disks loaded with the visual receptor rhodopsin. A wide range of genetic aberrations compromise ROS ultrastructure, impairing photoreceptor viability and function. Yet, the structural basis giving rise to the remarkable long range order of ROS membrane stacks and the molecular mechanisms underlying genetically inherited diseases remain elusive. Here, cryo-electron tomography (cryo-ET) performed on native ROS at molecular resolution provides insights into key structural determinants of ROS membrane architecture. Our data reveal the existence of two molecular connectors/spacers which likely contribute to the nanometer scale precise stacking of the ROS disks. We further show that the extreme radius of curvature at the disk rims is enforced by a continuous supramolecular assembly composed of peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) tetramers. We suggest that, together these molecular assemblies constitute the structural basis of the highly specialized ROS functional architecture. Cryo-ET therefore provides novel quantitative and structural information on the molecular architecture in ROS and insights into possible mechanisms underlying pathologies of certain PRPH2 mutations leading to blindness.

scholarly journals KINETICS OF ROD OUTER SEGMENT RENEWAL IN THE DEVELOPING MOUSE RETINA

1973 ◽  
Vol 58 (3) ◽  
pp. 650-661 ◽  
Author(s):  
Matthew M. LaVail
Keyword(s):  
Outer Segment ◽  
Photoreceptor Cells ◽  
Mouse Retina ◽  
Rod Photoreceptor ◽  
Adult Level ◽  
Rod Outer Segment ◽  
Equilibrium Length ◽  
Kinetics Of ◽  
Late Stages ◽  
Adult Rate

The kinetics of rod outer segment renewal in the developing retina have been investigated in C57BL/6J mice. Litters of mice were injected with [3H]amino acids at various ages and killed at progressively later time intervals. Plastic 1.5 µm sections of retina were studied by light microscope autoradiography. The rate of outer segment disk synthesis, as judged by labeled disk displacement away from the site of synthesis, is slightly greater than the adult level at 11–13 days of age; it rises to more than 1.6 times the adult rate between days 13 and 17, after which it falls to the adult level at 21–25 days. The rate of disk disposal, as measured by labeled disk movement toward the site of disposal, is less than 15% of the adult level at 11–13 days of age; it rises sharply to almost 70% of the adult level by days 13–15 and then more gradually approaches the adult rate. The net difference in rates of synthesis and disposal accounts for the rapid elongation of rod outer segments in the mouse between days 11 and 17 and the subsequent, more gradual elongation to the adult equilibrium length reached between days 19 and 25. The changing rate of outer segment disk synthesis characterizes the late stages of cytodifferentiation of the rod photoreceptor cells.

Structure and allosteric regulation of eukaryotic 6-phosphofructokinases

2013 ◽  
Vol 394 (8) ◽  
pp. 977-993 ◽  
Author(s):  
Torsten Schöneberg ◽  
Marco Kloos ◽  
Antje Brüser ◽  
Jürgen Kirchberger ◽  
Norbert Sträter
Keyword(s):  
Crystal Structures ◽  
Structural Information ◽  
Current Knowledge ◽  
Allosteric Regulation ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Directed Mutagenesis ◽  
Special Focus ◽  
Molecular Architecture ◽  
Key Enzyme

Abstract Although the crystal structures of prokaryotic 6-phosphofructokinase, a key enzyme of glycolysis, have been available for almost 25 years now, structural information about the more complex and highly regulated eukaryotic enzymes is still lacking until now. This review provides an overview of the current knowledge of eukaryotic 6-phosphofructokinase based on recent crystal structures, kinetic analyses and site-directed mutagenesis data with special focus on the molecular architecture and the structural basis of allosteric regulation.

scholarly journals Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6

2021 ◽  
Vol 5 (1) ◽  
pp. e202101149
Author(s):  
Yumiko Saijo-Hamano ◽  
Aalaa Alrahman Sherif ◽  
Ariel Pradipta ◽  
Miwa Sasai ◽  
Naoki Sakai ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Parasitophorous Vacuole ◽  
Membrane Binding ◽  
Structural Basis ◽  
In Silico Docking ◽  
Binding Interface ◽  
Dimerization Interface

The p47 immunity-related GTPase (IRG) Irgb6 plays a pioneering role in host defense against Toxoplasma gondii infection. Irgb6 is recruited to the parasitophorous vacuole membrane (PVM) formed by T. gondii and disrupts it. Despite the importance of this process, the molecular mechanisms accounting for PVM recognition by Irgb6 remain elusive because of lack of structural information on Irgb6. Here we report the crystal structures of mouse Irgb6 in the GTP-bound and nucleotide-free forms. Irgb6 exhibits a similar overall architecture to other IRGs in which GTP binding induces conformational changes in both the dimerization interface and the membrane-binding interface. The membrane-binding interface of Irgb6 assumes a unique conformation, composed of N- and C-terminal helical regions forming a phospholipid binding site. In silico docking of phospholipids further revealed membrane-binding residues that were validated through mutagenesis and cell-based assays. Collectively, these data demonstrate a novel structural basis for Irgb6 to recognize T. gondii PVM in a manner distinct from other IRGs.

scholarly journals Photosynthetic generation of oxygen

2008 ◽  
Vol 363 (1504) ◽  
pp. 2665-2674 ◽  
Author(s):  
James Barber
Keyword(s):  
Structural Information ◽  
Molecular Architecture ◽  
Oxygen Generation ◽  
X Ray Crystallography ◽  
Biological Studies ◽  
Wide Range ◽  
Photosynthetic Oxygen ◽  
Oxygen Evolving ◽  
Opening Up ◽  
Protein Environment

The oxygen in the atmosphere is derived from light-driven oxidation of water at a catalytic centre contained within a multi-subunit enzyme known as photosystem II (PSII). PSII is located in the photosynthetic membranes of plants, algae and cyanobacteria and its oxygen-evolving centre (OEC) consists of four manganese ions and a calcium ion surrounded by a highly conserved protein environment. Recently, the structure of PSII was elucidated by X-ray crystallography thus revealing details of the molecular architecture of the OEC. This structural information, coupled with an extensive knowledge base derived from a wide range of biophysical, biochemical and molecular biological studies, has provided a framework for understanding the chemistry of photosynthetic oxygen generation as well as opening up debate about its evolutionary origin.

scholarly journals Structural Basis for Innate Immune Sensing by M-ficolin and Its Control by a pH-dependent Conformational Switch

2007 ◽  
Vol 282 (49) ◽  
pp. 35814-35820 ◽  
Author(s):  
Virginie Garlatti ◽  
Lydie Martin ◽  
Evelyne Gout ◽  
Jean-Baptiste Reiser ◽  
Teizo Fujita ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Physiological Role ◽  
Innate Immune ◽  
Structural Basis ◽  
Structural Determinants ◽  
Conformational Switch ◽  
Binding Function ◽  
Monocytes And Macrophages ◽  
Immune Sensing ◽  
The One

Ficolins are soluble oligomeric proteins with lectin-like activity, assembled from collagen fibers prolonged by fibrinogen-like recognition domains. They act as innate immune sensors by recognizing conserved molecular markers exposed on microbial surfaces and thereby triggering effector mechanisms such as enhanced phagocytosis and inflammation. In humans, L- and H-ficolins have been characterized in plasma, whereas a third species, M-ficolin, is secreted by monocytes and macrophages. To decipher the molecular mechanisms underlying their recognition properties, we previously solved the structures of the recognition domains of L- and H-ficolins, in complex with various model ligands (Garlatti, V., Belloy, N., Martin, L., Lacroix, M., Matsushita, M., Endo, Y., Fujita, T., Fontecilla-Camps, J. C., Arlaud, G. J., Thielens, N. M., and Gaboriaud, C. (2007) EMBO J. 24, 623–633). We now report the ligand-bound crystal structures of the recognition domain of M-ficolin, determined at high resolution (1.75–1.8 Å), which provides the first structural insights into its binding properties. Interaction with acetylated carbohydrates differs from the one previously described for L-ficolin. This study also reveals the structural determinants for binding to sialylated compounds, a property restricted to human M-ficolin and its mouse counterpart, ficolin B. Finally, comparison between the ligand-bound structures obtained at neutral pH and nonbinding conformations observed at pH 5.6 reveals how the ligand binding site is dislocated at acidic pH. This means that the binding function of M-ficolin is subject to a pH-sensitive conformational switch. Considering that the homologous ficolin B is found in the lysosomes of activated macrophages (Runza, V. L., Hehlgans, T., Echtenacher, B., Zahringer, U., Schwaeble, W. J., and Mannel, D. N. (2006) J. Endotoxin Res. 12, 120–126), we propose that this switch could play a physiological role in such acidic compartments.

scholarly journals Raman Spectroscopic Imaging of Cholesterol and Docosahexaenoic Acid Distribution in the Retinal Rod Outer Segment

2011 ◽  
Vol 64 (5) ◽  
pp. 611 ◽  
Author(s):  
Zachary D. Schultz
Keyword(s):  
Docosahexaenoic Acid ◽  
Outer Segment ◽  
Rana Catesbeiana ◽  
Spectroscopic Imaging ◽  
Photoreceptor Cells ◽  
Integral Membrane Protein ◽  
Rod Photoreceptor ◽  
Rod Outer Segment ◽  
Cellular Processes ◽  
Retinal Rod

Raman vibrational spectroscopic imaging was performed on retinal rod cells isolated from bullfrogs (Rana catesbeiana). The Raman spectra enable determination of the lipid and protein rich rod outer segment (ROS) from the nucleus and inner segment of the cell. Peak fitting analysis of spectra obtained from individual rod photoreceptor cells show characteristic vibrational modes that can be associated with cholesterol and docosahexaenoic acid-containing lipids. These results provide direct observations of biomolecular gradients in the rod photoreceptor cells, which, thus far, have been based on indirect detergent extracts and histochemical analysis with indicators such as filipin. The detected biomolecules are associated with regulation of the integral membrane protein rhodopsin, and methods capable of direct observation of these biomolecules offer new routes to exploring their role in the regulation of cellular processes.

scholarly journals Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6

2021 ◽  
Author(s):  
Yumiko Saijo Hamano ◽  
Aalaa Alrahman Sherif ◽  
Ariel Pradipta ◽  
Miwa Sasai ◽  
Naoki Sakai ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Parasitophorous Vacuole ◽  
Membrane Binding ◽  
Structural Basis ◽  
In Silico Docking ◽  
Binding Interface ◽  
Toxoplasma Gondii Infection

The p47 immunity-related GTPase (IRG) Irgb6 plays a pioneering role in host defense against Toxoplasma gondii infection. It is recruited to the parasitophorous vacuole membrane (PVM) formed by T. gondii and disrupts it. Despite the importance of this process, the molecular mechanisms accounting for PVM recognition by Irgb6 remain elusive due to lack of structural information on Irgb6. Here we report the crystal structures of mouse Irgb6 in the GTP-bound and nucleotide-free forms. Irgb6 exhibits a similar overall architecture to other IRGs in which GTP-binding induces conformational changes in both the dimerization interface and the membrane-binding interface. The membrane-binding interface of Irgb6 assumes a unique conformation, composed of N- and C-terminal helical regions forming a phospholipid binding site. In silico docking of phospholipids further revealed membrane binding residues that were validated through mutagenesis and cell-based assays. Collectively, these data demonstrate a novel structural basis for Irgb6 to recognize T. gondii PVM in a manner distinct from other IRGs.

scholarly journals Structural basis underlying complex assembly and conformational transition of the type I R-M system

2017 ◽  
Vol 114 (42) ◽  
pp. 11151-11156 ◽  
Author(s):  
Yan-Ping Liu ◽  
Qun Tang ◽  
Jie-Zhong Zhang ◽  
Li-Fei Tian ◽  
Pu Gao ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Conformational Transition ◽  
Structural Information ◽  
Structural Basis ◽  
Type I ◽  
Structural Comparison ◽  
Complex Assembly ◽  
Adenosyl Methionine ◽  
Restriction Modification

Type I restriction-modification (R-M) systems are multisubunit enzymes with separate DNA-recognition (S), methylation (M), and restriction (R) subunits. Despite extensive studies spanning five decades, the detailed molecular mechanisms underlying subunit assembly and conformational transition are still unclear due to the lack of high-resolution structural information. Here, we report the atomic structure of a type I MTase complex (2M+1S) bound to DNA and cofactor S-adenosyl methionine in the “open” form. The intermolecular interactions between M and S subunits are mediated by a four-helix bundle motif, which also determines the specificity of the interaction. Structural comparison between open and previously reported low-resolution “closed” structures identifies the huge conformational changes within the MTase complex. Furthermore, biochemical results show that R subunits prefer to load onto the closed form MTase. Based on our results, we proposed an updated model for the complex assembly. The work reported here provides guidelines for future applications in molecular biology.

scholarly journals Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Agata Butryn ◽  
Jan M Schuller ◽  
Gabriele Stoehr ◽  
Petra Runge-Wollmann ◽  
Friedrich Förster ◽  
...  
Keyword(s):  
Structural Information ◽  
Structural Basis ◽  
Independent Manner ◽  
Histone Fold ◽  
Structural Framework ◽  
Wide Range ◽  
Transcription Complexes ◽  
Tata Box Binding Protein ◽  
Structural Mechanisms ◽  
Single Subunit

Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent remodeling reactions is largely absent. The single subunit remodeler Mot1 (modifier of transcription 1) dissociates TATA box-binding protein (TBP):DNA complexes, offering a useful system to address the structural mechanisms of Swi2/Snf2 ATPases. Here, we report the crystal structure of the N-terminal domain of Mot1 in complex with TBP, DNA, and the transcription regulator negative cofactor 2 (NC2). Our data show that Mot1 reduces DNA:NC2 interactions and unbends DNA as compared to the TBP:DNA:NC2 state, suggesting that Mot1 primes TBP:NC2 displacement in an ATP-independent manner. Electron microscopy and cross-linking data suggest that the Swi2/Snf2 domain of Mot1 associates with the upstream DNA and the histone fold of NC2, thereby revealing parallels to some nucleosome remodelers. This study provides a structural framework for how a Swi2/Snf2 ATPase interacts with its substrate DNA:protein complex.

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