Bacterial chromosome organization by collective dynamics of SMC condensins

A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various nucleoid-associated proteins, including the ATPase Structural Maintenance of Chromosomes (SMC) condensin. Although the molecular structure of these ATPases has been mapped in detail, it still remains unclear by which physical mechanisms they collectively generate long-range chromosomal contacts. Here, we develop a computational model that captures the subtle interplay between molecular-scale activity of slip-links and large-scale chromosome organization. We first consider a scenario in which the ATPase activity of slip-links regulates their DNA-recruitment near the origin of replication, while the slip-link dynamics is assumed to be diffusive. We find that such diffusive slip-links can collectively organize the entire chromosome into a state with aligned arms, but not within physiological constraints. However, slip-links that include motor activity are far more effective at organizing the entire chromosome over all length-scales. The persistence of motor slip-links at physiological densities can generate large, nested loops and drive them into the bulk of the DNA. Finally, our model with motor slip-links can quantitatively account for the rapid arm–arm alignment of chromosomal arms observed in vivo .

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Dynamics of putative raft-associated proteins at the cell surface

The Journal of Cell Biology ◽

10.1083/jcb.200312170 ◽

2004 ◽

Vol 165 (5) ◽

pp. 735-746 ◽

Cited By ~ 329

Author(s):

Anne K. Kenworthy ◽

Benjamin J. Nichols ◽

Catha L. Remmert ◽

Glenn M. Hendrix ◽

Mukesh Kumar ◽

...

Keyword(s):

Cell Surface ◽

Lipid Rafts ◽

Long Range ◽

Dominant Factor ◽

Membrane Microdomains ◽

Cholesterol Depletion ◽

Biochemical Fractionation ◽

Associated Proteins ◽

Raft Domains

Lipid rafts are conceptualized as membrane microdomains enriched in cholesterol and glycosphingolipid that serve as platforms for protein segregation and signaling. The properties of these domains in vivo are unclear. Here, we use fluorescence recovery after photobleaching to test if raft association affects a protein's ability to laterally diffuse large distances across the cell surface. The diffusion coefficients (D) of several types of putative raft and nonraft proteins were systematically measured under steady-state conditions and in response to raft perturbations. Raft proteins diffused freely over large distances (>4 μm), exhibiting Ds that varied 10-fold. This finding indicates that raft proteins do not undergo long-range diffusion as part of discrete, stable raft domains. Perturbations reported to affect lipid rafts in model membrane systems or by biochemical fractionation (cholesterol depletion, decreased temperature, and cholesterol loading) had similar effects on the diffusional mobility of raft and nonraft proteins. Thus, raft association is not the dominant factor in determining long-range protein mobility at the cell surface.

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The physical mechanisms that initiate and drive solar eruptions

Proceedings of the International Astronomical Union ◽

10.1017/s1743921313010958 ◽

2013 ◽

Vol 8 (S300) ◽

pp. 184-196 ◽

Cited By ~ 24

Author(s):

Guillaume Aulanier

Keyword(s):

Magnetic Fields ◽

Long Range ◽

Large Scale ◽

State Of The Art ◽

Flux Emergence ◽

Physical Mechanisms ◽

Driving Mechanisms ◽

Coronal Magnetic Fields ◽

Solar Eruptions

AbstractSolar eruptions are due to a sudden destabilization of force-free coronal magnetic fields. But the detailed mechanisms which can bring the corona towards an eruptive stage, then trigger and drive the eruption, and finally make it explosive, are not fully understood. A large variety of storage-and-release models have been developed and opposed to each other since 40 years. For example, photospheric flux emergence vs. flux cancellation, localized coronal reconnection vs. large-scale ideal instabilities and loss of equilibria, tether-cutting vs. breakout reconnection, and so on. The competition between all these approaches has led to a tremendous drive in developing and testing all these concepts, by coupling state-of-the-art models and observations. Thanks to these developments, it now becomes possible to compare all these models with one another, and to revisit their interpretation in light of their common and their different behaviors. This approach leads me to argue that no more than two distinct physical mechanisms can actually initiate and drive prominence eruptions: the magnetic breakout and the torus instability. In this view, all other processes (including flux emergence, flux cancellation, flare reconnection and long-range couplings) should be considered as various ways that lead to, or that strengthen, one of the aforementioned driving mechanisms.

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HupB Is a Bacterial Nucleoid-Associated Protein with an Indispensable Eukaryotic-Like Tail

mBio ◽

10.1128/mbio.01272-17 ◽

2017 ◽

Vol 8 (6) ◽

Cited By ~ 21

Author(s):

Joanna Hołówka ◽

Damian Trojanowski ◽

Katarzyna Ginda ◽

Bartosz Wojtaś ◽

Bartłomiej Gielniewski ◽

...

Keyword(s):

Cell Cycle ◽

Mycobacterium Tuberculosis ◽

Drug Development ◽

Health Problem ◽

Biological Function ◽

Multidrug Resistant ◽

Chromosome Organization ◽

Terminal Domain ◽

Associated Proteins

ABSTRACT In bacteria, chromosomal DNA must be efficiently compacted to fit inside the small cell compartment while remaining available for the proteins involved in replication, segregation, and transcription. Among the nucleoid-associated proteins (NAPs) responsible for maintaining this highly organized and yet dynamic chromosome structure, the HU protein is one of the most conserved and highly abundant. HupB, a homologue of HU, was recently identified in mycobacteria. This intriguing mycobacterial NAP is composed of two domains: an N-terminal domain that resembles bacterial HU, and a long and distinctive C-terminal domain that contains several PAKK/KAAK motifs, which are characteristic of the H1/H5 family of eukaryotic histones. In this study, we analyzed the in vivo binding of HupB on the chromosome scale. By using PALM (photoactivated localization microscopy) and ChIP-Seq (chromatin immunoprecipitation followed by deep sequencing), we observed that the C-terminal domain is indispensable for the association of HupB with the nucleoid. Strikingly, the in vivo binding of HupB displayed a bias from the origin (oriC) to the terminus (ter) of the mycobacterial chromosome (numbers of binding sites decreased toward ter). We hypothesized that this binding mode reflects a role for HupB in organizing newly replicated oriC regions. Thus, HupB may be involved in coordinating replication with chromosome segregation. IMPORTANCE We currently know little about the organization of the mycobacterial chromosome and its dynamics during the cell cycle. Among the mycobacterial nucleoid-associated proteins (NAPs) responsible for chromosome organization and dynamics, HupB is one of the most intriguing. It contains a long and distinctive C-terminal domain that harbors several PAKK/KAAK motifs, which are characteristic of the eukaryotic histone H1/H5 proteins. The HupB protein is also known to be crucial for the survival of tubercle bacilli during infection. Here, we provide in vivo experimental evidence showing that the C-terminal domain of HupB is crucial for its DNA binding. Our results suggest that HupB may be involved in organizing newly replicated regions and could help coordinate chromosome replication with segregation. Given that tuberculosis (TB) remains a serious worldwide health problem (10.4 million new TB cases were diagnosed in 2015, according to WHO) and new multidrug-resistant Mycobacterium tuberculosis strains are continually emerging, further studies of the biological function of HupB are needed to determine if this protein could be a prospect for novel antimicrobial drug development. IMPORTANCE We currently know little about the organization of the mycobacterial chromosome and its dynamics during the cell cycle. Among the mycobacterial nucleoid-associated proteins (NAPs) responsible for chromosome organization and dynamics, HupB is one of the most intriguing. It contains a long and distinctive C-terminal domain that harbors several PAKK/KAAK motifs, which are characteristic of the eukaryotic histone H1/H5 proteins. The HupB protein is also known to be crucial for the survival of tubercle bacilli during infection. Here, we provide in vivo experimental evidence showing that the C-terminal domain of HupB is crucial for its DNA binding. Our results suggest that HupB may be involved in organizing newly replicated regions and could help coordinate chromosome replication with segregation. Given that tuberculosis (TB) remains a serious worldwide health problem (10.4 million new TB cases were diagnosed in 2015, according to WHO) and new multidrug-resistant Mycobacterium tuberculosis strains are continually emerging, further studies of the biological function of HupB are needed to determine if this protein could be a prospect for novel antimicrobial drug development.

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Long-range order from local interactions: organization and development of distributed cortical networks

10.1101/335828 ◽

2018 ◽

Author(s):

Gordon B. Smith ◽

Bettina Hein ◽

David E. Whitney ◽

David Fitzpatrick ◽

Matthias Kaschube

Keyword(s):

Visual Cortex ◽

Spontaneous Activity ◽

Long Range ◽

Network Structure ◽

Large Scale ◽

Wide Field ◽

Cortical Networks ◽

Subsequent Formation ◽

Correlated Activity

The cortical networks that underlie behavior exhibit an orderly functional organization at local and global scales, which is readily evident in the visual cortex of carnivores and primates1-6. Here, neighboring columns of neurons represent the full range of stimulus orientations and contribute to distributed networks spanning several millimeters2,7-11. However, the principles governing functional interactions that bridge this fine-scale functional architecture and distant network elements are unclear, and the emergence of these network interactions during development remains unexplored. Here, by using in vivo wide-field and 2-photon calcium imaging of spontaneous activity patterns in mature ferret visual cortex, we find widespread and specific modular correlation patterns that accurately predict the local structure of visually-evoked orientation columns from the spontaneous activity of neurons that lie several millimeters away. The large-scale networks revealed by correlated spontaneous activity show abrupt ‘fractures’ in continuity that are in tight register with evoked orientation pinwheels. Chronic in vivo imaging demonstrates that these large-scale modular correlation patterns and fractures are already present at early stages of cortical development and predictive of the mature network structure. Silencing feed-forward drive through either retinal or thalamic blockade does not affect network structure suggesting a cortical origin for this large-scale correlated activity, despite the immaturity of long-range horizontal network connections in the early cortex. Using a circuit model containing only local connections, we demonstrate that such a circuit is sufficient to generate large-scale correlated activity, while also producing correlated networks showing strong fractures, a reduced dimensionality, and an elongated local correlation structure, all in close agreement with our empirical data. These results demonstrate the precise local and global organization of cortical networks revealed through correlated spontaneous activity and suggest that local connections in early cortical circuits may generate structured long-range network correlations that underlie the subsequent formation of visually-evoked distributed functional networks.

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Nucleoid associated proteins and their effect on E. coli chromosome

10.1101/2020.11.05.369934 ◽

2020 ◽

Author(s):

Ankit Gupta ◽

Abdul Wasim ◽

Jagannath Mondal

Keyword(s):

Long Range ◽

Short Range ◽

Computational Method ◽

Bacterial Chromosome ◽

Chromosome Organization ◽

E Coli ◽

Complex Interactions ◽

Long Range Interactions ◽

Associated Proteins ◽

Mutant Cells

AbstractA seemingly random and disorganized bacterial chromosome, in reality, is a well organized nucleus-like structure, called the nucleoid, which is maintained by several nucleoid associated proteins(NAPs). Here we present an application of a previously developed Hi-C based computational method to study the effects of some of these proteins on the E. coli chromosome. Simulations with encoded Hi-C data for mutant, hupAB deficient, E. coli cells, revealed a decondensed, axially expanded chromosome with enhanced short range and diminished long range interactions. Simulations for mutant cells deficient in FIS protein revealed that the effects are similar to that of the hupAB mutant, but the absence of FIS led to a greater disruption in chromosome organization. Absence of another NAP, MatP, known to mediate Ter macrodomain isolation, led to enhanced contacts between Ter and its flanking macrodomains but lacked any change in matS sites’ localization. Deficiency of MukBEF, the only SMC complex present in E. coli, led to disorganization of macrodomains. Upon further analysis, it was observed that the above mutations do not significantly impact the local chromosome organization (~ 100 Kb) but only affect the chromosome on a larger scale (>100 Kb). These observations shed more light on the sparsely explored effects of NAPs on the overall chromosome organization and helps us understand the myriad complex interactions NAPs have with the chromosome.

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A genome-wide interactome of DNA-associated proteins in the human liver

10.1101/111385 ◽

2017 ◽

Cited By ~ 2

Author(s):

Ryne C. Ramaker ◽

Daniel Savic ◽

Andrew A. Hardigan ◽

Kimberly Newberry ◽

Gregory M. Cooper ◽

...

Keyword(s):

Cell Lines ◽

Liver Tissue ◽

Human Liver ◽

Large Scale ◽

Healthy Human ◽

Binding Data ◽

A Genome ◽

Associated Proteins ◽

The Impact

AbstractLarge-scale efforts like the Encyclopedia of DNA Elements (ENCODE) Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology deviate in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation. Here we analyze ChIP-seq data for 20 DAPs assayed in two healthy human liver tissue samples, identifying more than 450,000 binding sites. We integrated binding data with transcriptome and phased whole genome data to investigate allelic DAP interactions and the impact of heterozygous sequence variation on the expression of neighboring genes. We find our tissue-based dataset demonstrates binding patterns more consistent with liver biology than cell lines, and describe uses of these data to better prioritize impactful non-coding variation. Collectively, our rich dataset offers novel insights into genome function in healthy liver tissue and provides a valuable research resource for assessing disease-related disruptions.

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In vivo metabolic labeling of sialoglycans in the mouse brain by using a liposome-assisted bioorthogonal reporter strategy

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1516524113 ◽

2016 ◽

Vol 113 (19) ◽

pp. 5173-5178 ◽

Cited By ~ 67

Author(s):

Ran Xie ◽

Lu Dong ◽

Yifei Du ◽

Yuntao Zhu ◽

Rui Hua ◽

...

Keyword(s):

Sialic Acid ◽

Mouse Brain ◽

Large Scale ◽

Neuronal Cell ◽

Brain Regions ◽

Metabolic Labeling ◽

Proteomic Profiling ◽

Associated Proteins ◽

Sialylated Glycoproteins

Mammalian brains are highly enriched with sialoglycans, which have been implicated in brain development and disease progression. However, in vivo labeling and visualization of sialoglycans in the mouse brain remain a challenge because of the blood−brain barrier. Here we introduce a liposome-assisted bioorthogonal reporter (LABOR) strategy for shuttling 9-azido sialic acid (9AzSia), a sialic acid reporter, into the brain to metabolically label sialoglycoconjugates, including sialylated glycoproteins and glycolipids. Subsequent bioorthogonal conjugation of the incorporated 9AzSia with fluorescent probes via click chemistry enabled fluorescence imaging of brain sialoglycans in living animals and in brain sections. Newly synthesized sialoglycans were found to widely distribute on neuronal cell surfaces, in particular at synaptic sites. Furthermore, large-scale proteomic profiling identified 140 brain sialylated glycoproteins, including a wealth of synapse-associated proteins. Finally, by performing a pulse−chase experiment, we showed that dynamic sialylation is spatially regulated, and that turnover of sialoglycans in the hippocampus is significantly slower than that in other brain regions. The LABOR strategy provides a means to directly visualize and monitor the sialoglycan biosynthesis in the mouse brain and will facilitate elucidating the functional role of brain sialylation.

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Effect of Synaptic Connectivity on Long-Range Synchronization of Fast Cortical Oscillations

Journal of Neurophysiology ◽

10.1152/jn.90613.2008 ◽

2008 ◽

Vol 100 (3) ◽

pp. 1562-1575 ◽

Cited By ~ 33

Author(s):

M. Bazhenov ◽

N. F. Rulkov ◽

I. Timofeev

Keyword(s):

Long Range ◽

Cognitive Processing ◽

Large Scale ◽

Phase Synchronization ◽

Critical Role ◽

Network Models ◽

Gamma Oscillations ◽

Common Mechanism ◽

Sensory Stimuli

Cortical gamma oscillations in the 20- to 80-Hz range are associated with attentiveness and sensory perception and have strong connections to both cognitive processing and temporal binding of sensory stimuli. These gamma oscillations become synchronized within a few milliseconds over distances spanning a few millimeters in spite of synaptic delays. In this study using in vivo recordings and large-scale cortical network models, we reveal a critical role played by the network geometry in achieving precise long-range synchronization in the gamma frequency band. Our results indicate that the presence of many independent synaptic pathways in a two-dimensional network facilitate precise phase synchronization of fast gamma band oscillations with nearly zero phase delays between remote network sites. These findings predict a common mechanism of precise oscillatory synchronization in neuronal networks.

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Purification of the Antihemophilic Factor by Gel Filtration on Agarose

Thrombosis and Haemostasis ◽

10.1055/s-0038-1651394 ◽

1969 ◽

Vol 22 (03) ◽

pp. 577-583 ◽

Cited By ~ 3

Author(s):

M.M.P Paulssen ◽

A.C.M.G.B Wouterlood ◽

H.L.M.A Scheffers

Keyword(s):

Factor Viii ◽

Plasma Proteins ◽

Large Scale ◽

Gel Filtration ◽

Large Scale Preparation ◽

Scale Preparation ◽

Antihemophilic Factor

SummaryFactor VIII can be isolated from plasma proteins, including fibrinogen by chromatography on agarose. The best results were obtained with Sepharose 6B. Large scale preparation is also possible when cryoprecipitate is separated by chromatography. In most fractions containing factor VIII a turbidity is observed which may be due to the presence of chylomicrons.The purified factor VIII was active in vivo as well as in vitro.

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The Effect of Active Site-inhibited Factor VIIa on Tissue Factor-initiated Coagulation Using Platelets before and after Aspirin Administration

Thrombosis and Haemostasis ◽

10.1055/s-0038-1657715 ◽

1997 ◽

Vol 78 (04) ◽

pp. 1202-1208 ◽

Cited By ~ 18

Author(s):

Marianne Kjalke ◽

Julie A Oliver ◽

Dougald M Monroe ◽

Maureane Hoffman ◽

Mirella Ezban ◽

...

Keyword(s):

Tissue Factor ◽

Active Site ◽

Large Scale ◽

Thrombin Generation ◽

Factor Viia ◽

Dependent Manner ◽

Antithrombotic Agent ◽

Before And After ◽

Ic50 Values

SummaryActive site-inactivated factor VIIa has potential as an antithrombotic agent. The effects of D-Phe-L-Phe-L-Arg-chloromethyl ketone-treated factor VIla (FFR-FVIIa) were evaluated in a cell-based system mimicking in vivo initiation of coagulation. FFR-FVIIa inhibited platelet activation (as measured by expression of P-selectin) and subsequent large-scale thrombin generation in a dose-dependent manner with IC50 values of 1.4 ± 0.8 nM (n = 8) and 0.9 ± 0.7 nM (n = 7), respectively. Kd for factor VIIa binding to monocytes ki for FFR-FVIIa competing with factor VIIa were similar (11.4 ± 0.8 pM and 10.6 ± 1.1 pM, respectively), showing that FFR-FVIIa binds to tissue factor in the tenase complex with the same affinity as factor VIIa. Using platelets from volunteers before and after ingestion of aspirin (1.3 g), there were no significant differences in the IC50 values of FFR-FVIIa [after aspirin ingestion, the IC50 values were 1.7 ± 0.9 nM (n = 8) for P-selectin expression, p = 0.37, and 1.4 ± 1.3 nM (n = 7) for thrombin generation, p = 0.38]. This shows that aspirin treatment of platelets does not influence the inhibition of tissue factor-initiated coagulation by FFR-FVIIa, probably because thrombin activation of platelets is not entirely dependent upon expression of thromboxane A2.

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