keyword
MENU ▼
Read by QxMD icon Read
search

cryo electron tomography

keyword
https://www.readbyqxmd.com/read/28496159/a-comprehensive-guide-to-pilus-biogenesis-in-gram-negative-bacteria
#1
REVIEW
Manuela K Hospenthal, Tiago R D Costa, Gabriel Waksman
Pili are crucial virulence factors for many Gram-negative pathogens. These surface structures provide bacteria with a link to their external environments by enabling them to interact with, and attach to, host cells, other surfaces or each other, or by providing a conduit for secretion. Recent high-resolution structures of pilus filaments and the machineries that produce them, namely chaperone-usher pili, type IV pili, conjugative type IV secretion pili and type V pili, are beginning to explain some of the intriguing biological properties that pili exhibit, such as the ability of chaperone-usher pili and type IV pili to stretch in response to external forces...
May 12, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28486768/the-trans-envelope-architecture-and-function-of-the-type-2-secretion-system-new-insights-raising-new-questions
#2
REVIEW
Jenny-Lee Thomassin, Javier Santos Moreno, Ingrid Guilvout, Guy Tran Van Nhieu, Olivera Francetic
Nanomachines belonging to the type IV filament (Tff) superfamily serve a variety of cellular functions in prokaryotes, including motility, adhesion, electrical conductance, competence and secretion. The type 2 secretion system (T2SS) Tff member assembles a short filament called pseudopilus that promotes the secretion of folded proteins from the periplasm across the outer membrane of Gram-negative bacteria. A combination of structural, biochemical, imaging, computational and in vivo approaches had led to a working model for the assembled nanomachine...
May 9, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28456019/dual-host-specificity-of-phage-sp6-is-facilitated-by-tailspike-rotation
#3
Jiagang Tu, Taehyun Park, Dustin R Morado, Kelly T Hughes, Ian J Molineux, Jun Liu
Bacteriophage SP6 exhibits dual-host adsorption specificity. The SP6 tailspikes are recognized as important in host range determination but the mechanisms underlying dual host specificity are unknown. Cryo-electron tomography and sub-tomogram classification were used to analyze the SP6 virion with a particular focus on the interaction of tailspikes with host membranes. The SP6 tail is surrounded by six V-shaped structures that interconnect in forming a hand-over-hand hexameric garland. Each V-shaped structure consists of two trimeric tailspike proteins: gp46 and gp47, connected through the adaptor protein gp37...
April 26, 2017: Virology
https://www.readbyqxmd.com/read/28412289/structural-studies-of-the-endogenous-spliceosome-the-supraspliceosome
#4
REVIEW
Joseph Sperling, Ruth Sperling
Pre-mRNA splicing is executed in mammalian cell nuclei within a huge (21MDa) and highly dynamic molecular machine - the supraspliceosome - that individually package pre-mRNA transcripts of different sizes and number of introns into complexes of a unique structure, indicating their universal nature. Detailed structural analysis of this huge and complex structure requires a stepwise approach using hybrid methods. Structural studies of the supraspliceosome by room temperature electron tomography, cryo-electron tomography, and scanning transmission electron microscope mass measurements revealed that it is composed of four native spliceosomes, each resembling an in vitro assembled spliceosome, which are connected by the pre-mRNA...
April 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28393831/determining-the-bacterial-cell-biology-of-planctomycetes
#5
Christian Boedeker, Margarete Schüler, Greta Reintjes, Olga Jeske, Muriel C F van Teeseling, Mareike Jogler, Patrick Rast, Daniela Borchert, Damien P Devos, Martin Kucklick, Miroslava Schaffer, Roberto Kolter, Laura van Niftrik, Susanne Engelmann, Rudolf Amann, Manfred Rohde, Harald Engelhardt, Christian Jogler
Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools. Here we develop methods for expression of fluorescent proteins and for gene deletion in a model planctomycete, Planctopirus limnophila, to analyse its cell organization in detail...
April 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28389960/structure-of-the-sodium-driven-flagellar-motor-in-marine-vibrio
#6
Yasuhiro Onoue, Michio Homma
Most bacteria can swim by rotating the flagellum. The basal body of the flagellum is an essential part for this motor function. Recent comprehensive analysis of the flagellar basal body structures across bacteria by cryo-electron tomography has revealed that they all share core structures, the rod, and rings: the C ring, M ring, S ring, L ring, and P ring. Furthermore, it also has uncovered that in some bacteria, there are extra ring structures in the periplasmic space and outer-membrane. Here, we describe a protocol to isolate the basal body of the flagellar basal body from a marine bacterium, Vibrio alginolyticus, for structural analysis of additional ring structures, the T ring and H ring...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28389958/in-situ-structural-analysis-of-the-spirochetal-flagellar-motor-by-cryo-electron-tomography
#7
Shiwei Zhu, Zhuan Qin, Juyu Wang, Dustin R Morado, Jun Liu
The bacterial flagellar motor is a large multi-component molecular machine. Structural determination of such a large complex is often challenging and requires extensive structural analysis in situ. Cryo-electron tomography (cryo-ET) has emerged as a powerful technique that enables us to visualize intact flagellar motors in cells with unprecedented details. Here, we detail the procedure beginning with sample preparation, followed by data acquisition, tomographic reconstruction, sub-tomogram analysis, and ultimately visualization of the intact spirochetal flagellar motor in Borrelia burgdorferi...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28358387/bacterial-kinesin-light-chain-bklc-links-the-btub-cytoskeleton-to-membranes
#8
Lurlène Akendengue, Sylvain Trépout, Martín Graña, Alexis Voegele, Carsten Janke, Bertrand Raynal, Alexandre Chenal, Sergio Marco, Anne Marie Wehenkel
Bacterial kinesin light chain is a TPR domain-containing protein encoded by the bklc gene, which co-localizes with the bacterial tubulin (btub) genes in a conserved operon in Prosthecobacter. Btub heterodimers show high structural homology with eukaryotic tubulin and assemble into head-to-tail protofilaments. Intriguingly, Bklc is homologous to the light chain of the microtubule motor kinesin and could thus represent an additional eukaryotic-like cytoskeletal element in bacteria. Using biochemical characterization as well as cryo-electron tomography we show here that Bklc interacts specifically with Btub protofilaments, as well as lipid vesicles and could thus play a role in anchoring the Btub filaments to the membrane protrusions in Prosthecobacter where they specifically localize in vivo...
March 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28344036/focus-the-interface-between-data-collection-and-data-processing-in-cryo-em
#9
Nikhil Biyani, Ricardo D Righetto, Robert McLeod, Daniel Caujolle-Bert, Daniel Castano-Diez, Kenneth N Goldie, Henning Stahlberg
We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions...
March 23, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28339603/optimization-of-stem-imaging-conditions-for-cryo-tomography
#10
Kazuhiro Aoyama, Kotaro Nagano, Kaoru Mitsuoka
For three-dimensional analysis of cryo-specimens using tomography at low and medium magnifications, the use of STEM images has some important advantages over TEM. A clear understanding of the electron dose in STEM is essential for optimized cryo-microscopy so a dose estimation technique for STEM imaging has been developed. The STEM convergence angle was shown to have a large impact on the image quality, in particular on the signal-to-noise ratio in the acquired images. Importantly, there is a clear trade-off between good STEM spatial resolution in the images with a large convergence angle and the signal-to-noise ratio, which is improved by reducing the convergence angle as much as possible...
February 9, 2017: Microscopy
https://www.readbyqxmd.com/read/28332496/cell-free-reconstitution-reveals-centriole-cartwheel-assembly-mechanisms
#11
P Guichard, V Hamel, M Le Guennec, N Banterle, I Iacovache, V Nemčíková, I Flückiger, K N Goldie, H Stahlberg, D Lévy, B Zuber, P Gönczy
How cellular organelles assemble is a fundamental question in biology. The centriole organelle organizes around a nine-fold symmetrical cartwheel structure typically ∼100 nm high comprising a stack of rings that each accommodates nine homodimers of SAS-6 proteins. Whether nine-fold symmetrical ring-like assemblies of SAS-6 proteins harbour more peripheral cartwheel elements is unclear. Furthermore, the mechanisms governing ring stacking are not known. Here we develop a cell-free reconstitution system for core cartwheel assembly...
March 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28330771/deciphering-the-molecular-architecture-of-membrane-contact-sites-by-cryo-electron-tomography
#12
REVIEW
Javier Collado, Rubén Fernández-Busnadiego
At membrane contact sites (MCS) two cellular membranes form tight appositions that play critical roles in fundamental phenomena such as lipid metabolism or Ca(2+) homeostasis. The interest for these structures has surged in recent years, bringing about the characterization of a plethora of MCS-resident molecules. How those molecules are structurally organized at MCS remains enigmatic, limiting our understanding of MCS function. Whereas such molecular detail is obscured by conventional electron microscopy sample preparation, cryo-electron tomography (cryo-ET) allows high resolution imaging of cellular landscapes in close-to-native conditions...
March 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28323617/cryoem-structures-of-membrane-pore-and-prepore-complex-reveal-cytolytic-mechanism-of-pneumolysin
#13
Katharina van Pee, Alexander Neuhaus, Edoardo D'Imprima, Deryck J Mills, Werner Kühlbrandt, Özkan Yildiz
Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel...
March 21, 2017: ELife
https://www.readbyqxmd.com/read/28291359/challenges-of-integrating-stochastic-dynamics-and-cryo-electron-tomograms-in-whole-cell-simulations
#14
Tyler M Earnest, Reika Watanabe, John E Stone, Julia Mahamid, Wolfgang Baumeister, Elizabeth Villa, Zaida Luthey-Schulten
Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved stochastic simulations of whole cells has arisen, allowing the simulation of complex biochemical networks over cell cycle time scales using data taken from -omics, single molecule experiments, and in vitro kinetics. By using real cell geometry derived from cryo-ET data, we have the opportunity to imbue these highly detailed structural data-frozen in time-with realistic biochemical dynamics and investigate how cell structure affects the behavior of the embedded chemical reaction network...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28283066/inside-the-chamber-of-secrets-of-the-type-iii-secretion-system
#15
Eric Cascales
The bacterial type III secretion system is a specialized machine that injects effectors into eukaryotic cells to manipulate the host cell physiology. In this issue of Cell, Hu et al. use cryo-electron tomography to reveal an unprecedented level of details regarding the architecture of this machine and the conformational changes that occur during its assembly.
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28283062/in-situ-molecular-architecture-of-the-salmonella-type-iii-secretion-machine
#16
Bo Hu, Maria Lara-Tejero, Qingke Kong, Jorge E Galán, Jun Liu
Type III protein secretion systems have specifically evolved to deliver bacterially encoded proteins into target eukaryotic cells. The core elements of this multi-protein machine are the envelope-associated needle complex, the inner membrane export apparatus, and a large cytoplasmic sorting platform. Here, we report a high-resolution in situ structure of the Salmonella Typhimurium type III secretion machine obtained by high-throughput cryo-electron tomography and sub-tomogram averaging. Through molecular modeling and comparative analysis of machines assembled with protein-tagged components or from different deletion mutants, we determined the molecular architecture of the secretion machine in situ and localized its structural components...
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28281671/visualizing-adsorption-of-cyanophage-p-ssp7-onto-marine-prochlorococcus
#17
Kazuyoshi Murata, Qinfen Zhang, Jesús Gerardo Galaz-Montoya, Caroline Fu, Maureen L Coleman, Marcia S Osburne, Michael F Schmid, Matthew B Sullivan, Sallie W Chisholm, Wah Chiu
Marine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium Prochlorococcus MED4 and its associated cyanophage P-SSP7 have revealed complex gene expression dynamics once infection has begun, but the initial cyanophage-host interactions remain poorly understood. Here, we used single particle cryo-electron tomography (cryo-ET) to investigate cyanophage-host interactions in this model system, based on 170 cyanophage-to-host adsorption events...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28276027/analysis-of-mitochondrial-membrane-protein-complexes-by-electron-cryo-tomography
#18
Vicki A M Gold, Tobias Brandt, Laetitia Cavellini, Mickael M Cohen, Raffaele Ieva, Martin van der Laan
The visualization of membrane protein complexes in their natural membrane environment is a major goal in an emerging area of research termed structural cell biology. Such approaches provide important information on the spatial distribution of protein complexes in their resident cellular membrane systems and on the structural organization of multi-subunit membrane protein assemblies. We have developed a method to specifically label active membrane protein complexes in their native membrane environment with electron-dense nanoparticles coupled to an activating ligand, in order to visualize them by electron cryo-tomography...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28269599/simultaneous-reconstruction-and-segmentation-with-the-mumford-shah-functional-for-electron-tomography
#19
Li Shen, Eric Todd Quinto, Shiqiang Wang, Ming Jiang
Electron micrography (EM) is an important method for determining the three-dimensional (3D) structure of macromolecular complexes and biological specimens. But there are several limitations such as poor signal-to-noise, limitation on range of tilt angles and sub-region subject to electron exposure, unintentional movements of the specimen, with EM systems that make the reconstruction procedure a severely ill-posed problem. A different choice of reconstruction method may lead to different results and create different additional artifacts in reconstructed images...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28241138/the-molecular-architecture-of-lamins-in-somatic-cells
#20
Yagmur Turgay, Matthias Eibauer, Anne E Goldman, Takeshi Shimi, Maayan Khayat, Kfir Ben-Harush, Anna Dubrovsky-Gaupp, K Tanuj Sapra, Robert D Goldman, Ohad Medalia
The nuclear lamina is a fundamental constituent of metazoan nuclei. It is composed mainly of lamins, which are intermediate filament proteins that assemble into a filamentous meshwork, bridging the nuclear envelope and chromatin. Besides providing structural stability to the nucleus, the lamina is involved in many nuclear activities, including chromatin organization, transcription and replication. However, the structural organization of the nuclear lamina is poorly understood. Here we use cryo-electron tomography to obtain a detailed view of the organization of the lamin meshwork within the lamina...
March 1, 2017: Nature
keyword
keyword
76654
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"