Role of cryo-ET in membrane bioenergetics research

2013 ◽  
Vol 41 (5) ◽  
pp. 1227-1234 ◽  
Author(s):  
Karen M. Davies ◽  
Bertram Daum
Keyword(s):  
Spatial Organization ◽  
Electron Tomography ◽  
Protein Complexes ◽  
Mitochondrial Diseases ◽  
Atp Synthesis ◽  
Cellular Level ◽  
Molecular Organization ◽  
Cellular Context ◽  
Membrane Bound ◽  
The Individual

To truly understand bioenergetic processes such as ATP synthesis, membrane-bound substrate transport or flagellar rotation, systems need to be analysed in a cellular context. Cryo-ET (cryo-electron tomography) is an essential part of this process, as it is currently the only technique which can directly determine the spatial organization of proteins at the level of both the cell and the individual protein complexes. The need to assess bioenergetic processes at a cellular level is becoming more and more apparent with the increasing interest in mitochondrial diseases. In recent years, cryo-ET has contributed significantly to our understanding of the molecular organization of mitochondria and chloroplasts. The present mini-review first describes the technique of cryo-ET and then discusses its role in membrane bioenergetics specifically in chloroplasts and mitochondrial research.

scholarly journals Structural and functional analyses of photosystem II in the marine diatom Phaeodactylum tricornutum

2019 ◽  
Vol 116 (35) ◽  
pp. 17316-17322 ◽  
Author(s):  
Orly Levitan ◽  
Muyuan Chen ◽  
Xuyuan Kuang ◽  
Kuan Yu Cheong ◽  
Jennifer Jiang ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Spatial Organization ◽  
Higher Plants ◽  
Electron Tomography ◽  
Protein Complexes ◽  
Spatial Differentiation ◽  
Thylakoid Membranes ◽  
Marine Diatom ◽  
Red Algal ◽  
Antenna Proteins

A descendant of the red algal lineage, diatoms are unicellular eukaryotic algae characterized by thylakoid membranes that lack the spatial differentiation of stroma and grana stacks found in green algae and higher plants. While the photophysiology of diatoms has been studied extensively, very little is known about the spatial organization of the multimeric photosynthetic protein complexes within their thylakoid membranes. Here, using cryo-electron tomography, proteomics, and biophysical analyses, we elucidate the macromolecular composition, architecture, and spatial distribution of photosystem II complexes in diatom thylakoid membranes. Structural analyses reveal 2 distinct photosystem II populations: loose clusters of complexes associated with antenna proteins and compact 2D crystalline arrays of dimeric cores. Biophysical measurements reveal only 1 photosystem II functional absorption cross section, suggesting that only the former population is photosynthetically active. The tomographic data indicate that the arrays of photosystem II cores are physically separated from those associated with antenna proteins. We hypothesize that the islands of photosystem cores are repair stations, where photodamaged proteins can be replaced. Our results strongly imply convergent evolution between the red and the green photosynthetic lineages toward spatial segregation of dynamic, functional microdomains of photosystem II supercomplexes.

scholarly journals Molecular Architecture of the Human Prp19/CDC5L Complex

2010 ◽  
Vol 30 (9) ◽  
pp. 2105-2119 ◽  
Author(s):  
Michael Grote ◽  
Elmar Wolf ◽  
Cindy L. Will ◽  
Ira Lemm ◽  
Dmitry E. Agafonov ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Spatial Organization ◽  
Protein Complexes ◽  
Limited Proteolysis ◽  
Molecular Organization ◽  
Molecular Architecture ◽  
Catalytic Core ◽  
C Terminus ◽  
Catalytically Active ◽  
Asymmetric Shape

ABSTRACT Protein complexes containing Prp19 play a central role during catalytic activation of the spliceosome, and Prp19 and its related proteins are major components of the spliceosome's catalytic core RNP. To learn more about the spatial organization of the human Prp19 (hPrp19)/CDC5L complex, which is comprised of hPrp19, CDC5L, PRL1, AD002, SPF27, CTNNBL1, and HSP73, we purified native hPrp19/CDC5L complexes from HeLa cells stably expressing FLAG-tagged AD002 or SPF27. Stoichiometric analyses indicated that, like Saccharomyces cerevisiae NTC ( n ine t een c omplex), the human Prp19/CDC5L complex contains four copies of hPrp19. Salt treatment identified a stable core comprised of CDC5L, hPrp19, PRL1, and SPF27. Protein-protein interaction studies revealed that SPF27 directly interacts with each component of the hPrp19/CDC5L complex core and also elucidated several additional, previously unknown interactions between hPrp19/CDC5L complex components. Limited proteolysis of the hPrp19/CDC5L complex revealed a protease-resistant complex comprised of SPF27, the C terminus of CDC5L, and the N termini of PRL1 and hPrp19. Under the electron microscope, purified hPrp19/CDC5L complexes exhibit an elongated, asymmetric shape with a maximum dimension of ∼20 nm. Our findings not only elucidate the molecular organization of the hPrp19/CDC5L complex but also provide insights into potential protein-protein interactions at the core of the catalytically active spliceosome.

scholarly journals Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Wojciech Wietrzynski ◽  
Miroslava Schaffer ◽  
Dimitry Tegunov ◽  
Sahradha Albert ◽  
Atsuko Kanazawa ◽  
...  
Keyword(s):  
Single Molecule ◽  
Electron Tomography ◽  
Protein Complexes ◽  
Membrane Surface ◽  
Thylakoid Membranes ◽  
Surface Topology ◽  
Thylakoid Stacking ◽  
Molecular Forces ◽  
Photosynthetic Regulation ◽  
The Individual

Thylakoid membranes scaffold an assortment of large protein complexes that work together to harness the energy of light. It has been a longstanding challenge to visualize how the intricate thylakoid network organizes these protein complexes to finely tune the photosynthetic reactions. Previously, we used in situ cryo-electron tomography to reveal the native architecture of thylakoid membranes (Engel et al., 2015). Here, we leverage technical advances to resolve the individual protein complexes within these membranes. Combined with a new method to visualize membrane surface topology, we map the molecular landscapes of thylakoid membranes inside green algae cells. Our tomograms provide insights into the molecular forces that drive thylakoid stacking and reveal that photosystems I and II are strictly segregated at the borders between appressed and non-appressed membrane domains. This new approach to charting thylakoid topology lays the foundation for dissecting photosynthetic regulation at the level of single protein complexes within the cell.

scholarly journals Template-free detection and classification of heterogeneous membrane-bound complexes in cryo-electron tomograms

2018 ◽  
Author(s):  
Antonio Martinez-Sanchez ◽  
Zdravko Kochovski ◽  
Ulrike Laugks ◽  
Johannes Meyer zum Alten Borgloh ◽  
Saikat Chakraborty ◽  
...  
Keyword(s):  
De Novo ◽  
Electron Tomography ◽  
Protein Complexes ◽  
3D Structure ◽  
Unsupervised Classification ◽  
Molecular Architecture ◽  
Intact Cells ◽  
Heterogeneous Membrane ◽  
Membrane Bound ◽  
Template Free

AbstractWith faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography (cryo-ET) provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification. Applying this procedure to tomograms of intact cells and isolated endoplasmic reticulum (ER), we detected and classified small protein complexes like the ER protein translocons, which were not detected by other methods before. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Therefore the procedure presented allows a comprehensive detection and a structural analysis of complexes in their native state. In addition, we present structural evidence that different ribosome-free translocon species are present at the ER membrane, determine their 3D structure, and show that they have different localization patterns forming nanodomains.

Subcellular organization of snRNPS in mammalian cells

1995 ◽  
Vol 53 ◽  
pp. 772-773
Author(s):  
A. Gregory Matera
Keyword(s):  
Rna Processing ◽  
Cell Biology ◽  
Mammalian Cells ◽  
Spatial Organization ◽  
Protein Complexes ◽  
Nuclear Architecture ◽  
Valuable Insight ◽  
Subcellular Organization ◽  
Protein Components ◽  
The Individual

Our laboratory is interested in aspects of eukaryotic gene expression that may be regulated at the level of nuclear architecture and/or localization. Understanding the spatial organization of genes and gene products within mammalian nuclei will provide valuable insight into how the various metabolic processes such as replication, transcription, processing and transport are orchestrated. In order to begin to address these questions, we have chosen to study the cell biology of RNA processing. Small RNA-protein complexes known as ribonucleoproteins (RNPs) are central factors in numerous RNA processing reactions. Much of what is currently known about the subcellular organization of RNPs is based upon the locations of the protein components of RNPs, not the RNA components. Furthermore, since many RNAs share common protein subunits it is essential to develop probes which are specific to the individual RNAs. We utilize highly specific antisense oligonucleotide probes and fluorescence in situ hybridization (FISH) to ascertain the organization of RNPs and their associations with particular subdomains within mammalian cells.

Mitochondrial Disease

2021 ◽  
pp. 1126-1133
Author(s):  
Radhika Dhamija ◽  
Erin Conboy ◽  
Ralitza H. Gavrilova
Keyword(s):  
Oxidative Phosphorylation ◽  
Mitochondrial Membrane ◽  
Protein Complexes ◽  
Mitochondrial Diseases ◽  
Mendelian Inheritance ◽  
Inner Mitochondrial Membrane ◽  
Oxidative Phosphorylation System ◽  
Transport Chain ◽  
Membrane Bound ◽  
Multimeric Protein

Primary mitochondrial diseases are a heterogeneous group of disorders that result from defects of the oxidative phosphorylation system of the mitochondria. Often underrecognized, mitochondrial diseases are uncommon (estimated incidence, 1 in 10,000 live births). Mitochondria are double-membrane–bound cytoplasmic organelles whose primary function is to provide energy (ie, adenosine triphosphate [ATP]) from the breakdown of carbohydrates, protein, and lipids by means of the electron transport chain and the oxidative phosphorylation system. The respiratory chain of mitochondria, located in the inner mitochondrial membrane, consists of 5 multimeric protein complexes (complexes I-IV and ATP synthase [complex V]). The structural proteins of these complexes are encoded by both mitochondrial and nuclear genes. Therefore, primary mitochondrial disorders can follow a maternal or mendelian inheritance pattern.

scholarly journals Biosensors Monitor Ligand-Selective Effects at Kappa Opioid Receptors

2021 ◽  
Author(s):  
Lucie Oberhauser ◽  
Miriam Stoeber
Keyword(s):  
Subcellular Location ◽  
Receptor Activation ◽  
Cellular Level ◽  
Two Dimensions ◽  
Kappa Opioid Receptor ◽  
Kappa Opioid ◽  
Downstream Signaling ◽  
Regulator Protein ◽  
Cellular Context ◽  
Selective Effects

AbstractThe kappa opioid receptor (KOR) has emerged as a promising therapeutic target for pain and itch treatment. There is growing interest in biased agonists that preferentially activate select signaling pathways downstream of KOR activation on the cellular level due to their therapeutic promise in retaining the analgesic and antipruritic effects and eliminating the sedative and dysphoric effects of KOR signaling on the physiological level. The concept of ligand-selective signaling includes that biased ligands promote KOR to selectively recruit one transducer or regulator protein over another, introducing bias into the signaling cascade at the very receptor-proximal level. Measuring agonist effects directly at the receptor has remained challenging and previous studies have focused on inferring agonist-selective KOR engagement with G protein relative to β-arrestin based on downstream signaling readouts. Here we discuss novel strategies to directly assess ligand-selective effects on receptor activation using KOR-interacting biosensors. The conformation-specific cytoplasmic biosensors are disconnected from the endogenous signaling machinery and provide a direct receptor-proxy readout of ligand effects in living cells. Receptor–biosensor interaction is ligand concentration dependent and can be used to determine relative ligand potency and efficacy. In addition, the biosensors reveal the existence of two dimensions of agonist bias in the cellular context: Firstly, agonists can selectively produce discrete protein-engaged KOR states and secondly, agonists can differ in the precise subcellular location at which they activate KOR. We discuss the value and the limitations of using orthogonal receptor-interacting biosensors in the quest to understand functional selectivity amongst KOR agonists in the cellular context.

scholarly journals Mitochondrial microRNAs: A Putative Role in Tissue Regeneration

Biology ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 486
Author(s):  
Sílvia C. Rodrigues ◽  
Renato M. S. Cardoso ◽  
Filipe V. Duarte
Keyword(s):  
Tissue Regeneration ◽  
Protein Complexes ◽  
Mitochondrial Protein ◽  
Noncoding Rnas ◽  
Atp Synthesis ◽  
Mitochondrial Proteins ◽  
Cellular Mechanisms ◽  
Small Noncoding Rnas ◽  
Mitochondrial Ribosome

The most famous role of mitochondria is to generate ATP through oxidative phosphorylation, a metabolic pathway that involves a chain of four protein complexes (the electron transport chain, ETC) that generates a proton-motive force that in turn drives the ATP synthesis by the Complex V (ATP synthase). An impressive number of more than 1000 mitochondrial proteins have been discovered. Since mitochondrial proteins have a dual genetic origin, it is predicted that ~99% of these proteins are nuclear-encoded and are synthesized in the cytoplasmatic compartment, being further imported through mitochondrial membrane transporters. The lasting 1% of mitochondrial proteins are encoded by the mitochondrial genome and synthesized by the mitochondrial ribosome (mitoribosome). As a result, an appropriate regulation of mitochondrial protein synthesis is absolutely required to achieve and maintain normal mitochondrial function. Regarding miRNAs in mitochondria, it is well-recognized nowadays that several cellular mechanisms involving mitochondria are regulated by many genetic players that originate from either nuclear- or mitochondrial-encoded small noncoding RNAs (sncRNAs). Growing evidence collected from whole genome and transcriptome sequencing highlight the role of distinct members of this class, from short interfering RNAs (siRNAs) to miRNAs and long noncoding RNAs (lncRNAs). Some of the mechanisms that have been shown to be modulated are the expression of mitochondrial proteins itself, as well as the more complex coordination of mitochondrial structure and dynamics with its function. We devote particular attention to the role of mitochondrial miRNAs and to their role in the modulation of several molecular processes that could ultimately contribute to tissue regeneration accomplishment.

scholarly journals Probing the biogenesis pathway and dynamics of thylakoid membranes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tuomas Huokko ◽  
Tao Ni ◽  
Gregory F. Dykes ◽  
Deborah M. Simpson ◽  
Philip Brownridge ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Photosystem I ◽  
Spatial Organization ◽  
Electron Flux ◽  
Protein Complexes ◽  
Thylakoid Membranes ◽  
Thylakoid Biogenesis ◽  
Photosynthetic Complexes ◽  
Photosynthetic Machinery ◽  
Pcc 7942

AbstractHow thylakoid membranes are generated to form a metabolically active membrane network and how thylakoid membranes orchestrate the insertion and localization of protein complexes for efficient electron flux remain elusive. Here, we develop a method to modulate thylakoid biogenesis in the rod-shaped cyanobacterium Synechococcus elongatus PCC 7942 by modulating light intensity during cell growth, and probe the spatial-temporal stepwise biogenesis process of thylakoid membranes in cells. Our results reveal that the plasma membrane and regularly arranged concentric thylakoid layers have no physical connections. The newly synthesized thylakoid membrane fragments emerge between the plasma membrane and pre-existing thylakoids. Photosystem I monomers appear in the thylakoid membranes earlier than other mature photosystem assemblies, followed by generation of Photosystem I trimers and Photosystem II complexes. Redistribution of photosynthetic complexes during thylakoid biogenesis ensures establishment of the spatial organization of the functional thylakoid network. This study provides insights into the dynamic biogenesis process and maturation of the functional photosynthetic machinery.

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