scholarly journals Dynamic spatial organization of multi-protein complexes controlling microbial polar organization, chromosome replication, and cytokinesis

2012 ◽  
Author(s):  
Harley McAdams ◽  
Lucille Shapiro ◽  
Mark Horowitz ◽  
Gary Andersen ◽  
Kenneth Downing ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Protein Complexes ◽  
Chromosome Replication ◽  
Polar Organization

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.

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.

A Generic Strategy To Analyze the Spatial Organization of Multi-Protein Complexes by Cross-Linking and Mass Spectrometry

2000 ◽  
Vol 72 (2) ◽  
pp. 267-275 ◽  
Author(s):  
Juri Rappsilber ◽  
Symeon Siniossoglou ◽  
Eduard C. Hurt ◽  
Matthias Mann
Keyword(s):  
Mass Spectrometry ◽  
Spatial Organization ◽  
Protein Complexes ◽  
Cross Linking ◽  
Generic Strategy

scholarly journals Eisosome proteins assemble into a membrane scaffold

2011 ◽  
Vol 195 (5) ◽  
pp. 889-902 ◽  
Author(s):  
Lena Karotki ◽  
Juha T. Huiskonen ◽  
Christopher J. Stefan ◽  
Natasza E. Ziółkowska ◽  
Robyn Roth ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Self Assembly ◽  
Spatial Organization ◽  
Protein Complexes ◽  
Lipid Binding ◽  
Yeast Cells ◽  
Core Components ◽  
The Many ◽  
Plasma Membrane Domain ◽  
Membrane Scaffold

Spatial organization of membranes into domains of distinct protein and lipid composition is a fundamental feature of biological systems. The plasma membrane is organized in such domains to efficiently orchestrate the many reactions occurring there simultaneously. Despite the almost universal presence of membrane domains, mechanisms of their formation are often unclear. Yeast cells feature prominent plasma membrane domain organization, which is at least partially mediated by eisosomes. Eisosomes are large protein complexes that are primarily composed of many subunits of two Bin–Amphiphysin–Rvs domain–containing proteins, Pil1 and Lsp1. In this paper, we show that these proteins self-assemble into higher-order structures and bind preferentially to phosphoinositide-containing membranes. Using a combination of electron microscopy approaches, we generate structural models of Pil1 and Lsp1 assemblies, which resemble eisosomes in cells. Our data suggest that the mechanism of membrane organization by eisosomes is mediated by self-assembly of its core components into a membrane-bound protein scaffold with lipid-binding specificity.

scholarly journals The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression

2021 ◽  
Vol 12 ◽  
Author(s):  
Marios Agelopoulos ◽  
Spyros Foutadakis ◽  
Dimitris Thanos
Keyword(s):  
Gene Expression ◽  
Spatial Organization ◽  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Current View ◽  
Regulation Of Expression ◽  
Time Space ◽  
Transcriptional Regulatory ◽  
Immune Related Genes

Regulation of gene expression in time, space and quantity is orchestrated by the functional interplay of cis-acting elements and trans-acting factors. Our current view postulates that transcription factors recognize enhancer DNA and read the transcriptional regulatory code by cooperative DNA binding to specific DNA motifs, thus instructing the recruitment of transcriptional regulatory complexes forming a plethora of higher-ordered multi-protein-DNA and protein-protein complexes. Here, we reviewed the formation of multi-dimensional chromatin assemblies implicated in gene expression with emphasis on the regulatory role of enhancer hubs as coordinators of stochastic gene expression. Enhancer hubs contain many interacting regulatory elements and represent a remarkably dynamic and heterogeneous network of multivalent interactions. A functional consequence of such complex interaction networks could be that individual enhancers function synergistically to ensure coordination, tight control and robustness in regulation of expression of spatially connected genes. In this review, we discuss fundamental paradigms of such inter- and intra- chromosomal associations both in the context of immune-related genes and beyond.

The brain of the honeybee Apis mellifera . I. The connections and spatial organization of the mushroom bodies

1982 ◽  
Vol 298 (1091) ◽  
pp. 309-354 ◽  
Keyword(s):  
Visual Information ◽  
Spatial Organization ◽  
Short Term Memory ◽  
Single Layer ◽  
Mushroom Bodies ◽  
After Effects ◽  
Kenyon Cells ◽  
The Individual ◽  
Polar Organization ◽  
The Brain

The mushroom bodies of the bee are paired neuropils in the dorsal part of the brain. Each is composed of the arborizations of over 17 x 10 4 small interneurons of similar architecture called Kenyon cells. Golgi staining demonstrates that these neurons can be divided into five groups distinguished on the basis of their dendritic specializations and geometry. The mushroom body neuropils each consist of a pair of cup-shaped structures, the calyces, connected by two short fused stalks, the pedunculus, to two lobes, the α- and β-lobes. Each calyx is formed from three concentric neuropil zones, the basal ring, the collar and the lip. The calyces are organized in a polar fashion; within the calyces each of the five categories of Kenyon cell has a distribution limited to particular polar contours. The dendritic volumes of neighbouring Kenyon cells arborizing within each individual contour are greatly overlapped. Fibres from groups of neighbouring cells within a calycal contour are gathered into bundles that project into the pedunculus, each fibre dividing to enter both the the α- and β-lobes. The pedunculus and the lobes are conspicuously layered. Kenyon cells with neighbouring dendritic fields within the same calycal contour occupy a single layer in the pedunculus and lobes. Thus the two- polar organization of the calyces is transformed into a Cartesian map within the pedunculus, which continues into the α- and β-lobes. The calyx receives input fibres from both the antennal lobes and the optic neuropils. The branching patterns of these cells reflect the polar organization of the calyces as their terminals are restricted to one or more of the three gross compartments of the calycal neuropil. The course of these tracts and the morphologies of the fibres that they contain are described. Cells considered to represent outputs from the mushroom bodies arborize in the pedunculus and α- and β-lobes. Generally the arborizations of the output neurons reflect the layered organization of these neuropils. Fibres from the two lobes run to the anterior median and lateral protocerebral neuropil, and the anterior optic tubercle. Additionally there is an extensive network of feedback interneurons that inter- connect the α- and β-lobes with the ipsi- and contralateral calyces. Many individual neurons have branches in both the α- and β-lobes and in the pedunculus. The pathways and geometries of the fibres subserving the two lobes are described. The hypothesis of Vowles (1955) that the individual lobes represent a separation of sensory and motor output areas is shown to be incorrect. The anatomy of the bee’s mushroom bodies suggests that they process second-order antennal and fourth- and higher-order visual information. The feedback pathways are discussed as possible means of creating long-lasting after-effects which may be important in complex timing processes and possibly the formation of short-term memory.

scholarly journals mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction

2018 ◽  
Vol 217 (12) ◽  
pp. 4124-4140 ◽  
Author(s):  
Anthony Khong ◽  
Roy Parker
Keyword(s):  
Single Molecule ◽  
Mrna Stability ◽  
Rna Structure ◽  
Spatial Organization ◽  
Closed Loop ◽  
Protein Complexes ◽  
Loop Model ◽  
Reading Frame ◽  
Translation Inhibition ◽  
Changes Over Time

Stress granules (SGs) are transient membraneless organelles of nontranslating mRNA–protein complexes (mRNPs) that form during stress. In this study, we used multiple single-molecule FISH probes for particular mRNAs to examine their SG recruitment and spatial organization. Ribosome runoff is required for SG entry, as long open reading frame (ORF) mRNAs are delayed in SG accumulation, indicating that the SG transcriptome changes over time. Moreover, mRNAs are ∼20× compacted from an expected linear length when translating and compact ∼2-fold further in a stepwise manner beginning at the 5′ end during ribosome runoff. Surprisingly, the 5′ and 3′ ends of the examined mRNAs were separated when translating, but in nontranslating conditions the ends of long ORF mRNAs become close, suggesting that the closed-loop model of mRNPs preferentially forms on nontranslating mRNAs. Compaction of ribosome-free mRNAs is ATP independent, consistent with compaction occurring through RNA structure formation. These results suggest that translation inhibition triggers an mRNP reorganization that brings ends closer, which has implications for the regulation of mRNA stability and translation by 3′ UTR elements and the poly(A) tail.

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 Nanoscale subcellular architecture revealed by multicolor 3D salvaged fluorescence imaging

2019 ◽  
Author(s):  
Yongdeng Zhang ◽  
Lena K. Schroeder ◽  
Mark D. Lessard ◽  
Phylicia Kidd ◽  
Jeeyun Chung ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Cell Biology ◽  
Mammalian Cells ◽  
Spatial Organization ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Super Resolution ◽  
Membrane Structures ◽  
Molecular Specificity ◽  
20 Nm

AbstractCombining the molecular specificity of fluorescent probes with three-dimensional (3D) imaging at nanoscale resolution is critical for investigating the spatial organization and interactions of cellular organelles and protein complexes. We present a super-resolution light microscope that enables simultaneous multicolor imaging of whole mammalian cells at ~20 nm 3D resolution. We show its power for cell biology research with fluorescence images that resolved the highly convoluted Golgi apparatus and the close contacts between the endoplasmic reticulum and the plasma membrane, structures that have traditionally been the imaging realm of electron microscopy.One Sentence SummaryComplex cellular structures previously only resolved by electron microscopy can now be imaged in multiple colors by 4Pi-SMS.

Polarity of the ascidian egg cortex before fertilization

Development ◽  
1992 ◽  
Vol 115 (1) ◽  
pp. 221-237 ◽  
Author(s):  
C. Sardet ◽  
J. Speksnijder ◽  
M. Terasaki ◽  
P. Chang
Keyword(s):  
Spatial Organization ◽  
Cytochalasin B ◽  
Centrifugal Forces ◽  
Calcium Dependent ◽  
Isolated Cortex ◽  
Coated Surface ◽  
The Stability ◽  
Polar Organization ◽  
Polar Distribution ◽  
Egg Cortex

The unfertilized ascidian egg displays a visible polar organization along its animal-vegetal axis. In particular, the myoplasm, a mitochondria-rich subcortical domain inherited by the blastomeres that differentiate into muscle cells, is mainly situated in the vegetal hemisphere. We show that, in the unfertilized egg, this vegetal domain is enriched in actin and microfilaments and excludes microtubules. This polar distribution of microfilaments and microtubules persists in isolated cortices prepared by shearing eggs attached to a polylysine-coated surface. The isolated cortex is further characterized by an elaborate network of tubules and sheets of endoplasmic reticulum (ER). This cortical ER network is tethered to the plasma membrane at discrete sites, is covered with ribosomes and contains a calsequestrin-like protein. Interestingly, this ER network is distributed in a polar fashion along the animal-vegetal axis of the egg: regions with a dense network consisting mainly of sheets or tightly knit tubes are present in the vegetal hemisphere only, whereas areas characterized by a sparse tubular ER network are uniquely found in the animal hemisphere region. The stability of the polar organization of the cortex was studied by perturbing the distribution of organelles in the egg and depolymerizing microfilaments and microtubules. The polar organization of the cortical ER network persists after treatment of eggs with nocodazole, but is disrupted by treatment with cytochalasin B. In addition, we show that centrifugal forces that displace the cytoplasmic organelles do not alter the appearance and polar organization of the isolated egg cortex. These findings taken together with our previous work suggest that the intrinsic polar distribution of cortical membranous and cytoskeletal components along the animal-vegetal axis of the egg are important for the spatial organization of calcium-dependent events and their developmental consequences.

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