scholarly journals Whole-cell scale dynamic organization of lysosomes revealed by spatial statistical analysis

2017 ◽  
Author(s):  
Qinle Ba ◽  
Guruprasad Raghavan ◽  
Kirill Kiselyov ◽  
Ge Yang
Keyword(s):  
Collective Behavior ◽  
Spatial Organization ◽  
Cultured Cells ◽  
Single Cells ◽  
Eukaryotic Cells ◽  
Intracellular Space ◽  
Whole Cell ◽  
Spatial Statistical Analysis ◽  
Membrane Bound ◽  
Coordinated Effects

In eukaryotic cells, lysosomes are distributed in the cytoplasm as individual membrane-bound compartments to degrade macromolecules and to control cellular metabolism. A fundamental yet unanswered question is whether and, if so, how individual lysosomes are spatially organized so that their functions can be coordinated and integrated to meet changing needs of cells. To address this question, we analyze their collective behavior in cultured cells using spatial statistical techniques. We find that in single cells, lysosomes maintain nonrandom, stable, yet distinct spatial distributions, which are mediated by the coordinated effects of the cytoskeleton and lysosomal biogenesis on different lysosomal subpopulations. Furthermore, we find that throughout the intracellular space, lysosomes form dynamic clusters that substantially increase their interactions with endosomes. Together, our findings reveal the spatial organization of lysosomes at the whole-cell scale and provide new insights into how organelle interactions are mediated and regulated over the entire intracellular space.

scholarly journals AnIn-SilicoMammalian Whole-Cell Model Reveals the Influence of Spatial Organization on RNA Splicing Efficiency

2018 ◽  
Author(s):  
Zhaleh Ghaemia ◽  
Joseph R. Peterson ◽  
Martin Gruebele ◽  
Zaida Luthey-Schulten
Keyword(s):  
Experimental Data ◽  
Hela Cell ◽  
Rna Splicing ◽  
Spatial Organization ◽  
Cell Model ◽  
Stochastic Simulations ◽  
Eukaryotic Cells ◽  
Nuclear Pore ◽  
Whole Cell ◽  
Membrane Bound

Spatial organization is a characteristic of eukaryotic cells, achieved by utilizing both membrane-bound and non-bound organelles. We model the effects of this organization and of organelle heterogeneity on RNA splicing (the process of making translationally-ready messenger RNA) and on splicing particles (the building blocks of splicing machinery) in mammalian cells. We constructed a spatially-resolved whole HeLa cell model from various experimental data and developed reaction networks to describe the RNA splicing processes. We incorporated these networks into our whole-cell model and performed stochastic simulations for up to 15 minutes of biological time. We find that the number of nuclear pore complexes affects the number of assembled splicing particles; that a slight increase of splicing particle localization in nuclear speckles (non-membrane-bound or- ganelles) leads to disproportionate enhancement in the mRNA splicing and reduction in the transcript noise; and that compartmentalization is critical for a correctly-assembled particle yield. Our model also predicts that the distance between genes and speckles has a considerable effect on effective mRNA production rate, further emphasizing the importance of genome organization around speckles. The HeLa cell model, including organelles and subcompartments, provides an adaptable foundation to study other cellular processes which are strongly modulated by spatio-temporal heterogeneity.Significance StatementThe spliceosome is one of the most complex cellular machineries that cuts and splices the RNA code in eukaryotic cells. It dynamically assembles, disassembles, and its components are formed in multiple compartments. The efficiency of splicing process depends on localization of its components in nuclear membrane-less organelles. Therefore, a computational model of spliceosomal function must contain a spatial model of the entire cell. However, building such a model is a challenging task, mainly due to the lack of homogeneous experimental data and a suitable computational framework. Here, we overcome these challenges and present a whole HeLa cell model, with nuclear, subnuclear, and extensive cytoplasmic structures. The three-dimensional model is supplemented by reaction-diffusion processes to shed light on the function of the spliceosome.

scholarly journals Restricted Localization of Photosynthetic Intracytoplasmic Membranes (ICMs) in Multiple Genera of Purple Nonsulfur Bacteria

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Breah LaSarre ◽  
David T. Kysela ◽  
Barry D. Stein ◽  
Adrien Ducret ◽  
Yves V. Brun ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Light Harvesting ◽  
Single Cells ◽  
Photosynthetic Pigment ◽  
Live Cells ◽  
Purple Nonsulfur Bacteria ◽  
Intracytoplasmic Membrane ◽  
Intracellular Space ◽  
Evolutionary Relatedness ◽  
Membrane Bound

ABSTRACTIn bacteria and eukaryotes alike, proper cellular physiology relies on robust subcellular organization. For the phototrophic purple nonsulfur bacteria (PNSB), this organization entails the use of a light-harvesting, membrane-bound compartment known as the intracytoplasmic membrane (ICM). Here we show that ICMs are spatially and temporally localized in diverse patterns among PNSB. We visualized ICMs in live cells of 14 PNSB species across nine genera by exploiting the natural autofluorescence of the photosynthetic pigment bacteriochlorophyll (BChl). We then quantitatively characterized ICM localization using automated computational analysis of BChl fluorescence patterns within single cells across the population. We revealed that while many PNSB elaborate ICMs along the entirety of the cell, species across as least two genera restrict ICMs to discrete, nonrandom sites near cell poles in a manner coordinated with cell growth and division. Phylogenetic and phenotypic comparisons established that ICM localization and ICM architecture are not strictly interdependent and that neither trait fully correlates with the evolutionary relatedness of the species. The natural diversity of ICM localization revealed herein has implications for both the evolution of phototrophic organisms and their light-harvesting compartments and the mechanisms underpinning spatial organization of bacterial compartments.IMPORTANCEMany bacteria organize their cellular space by constructing subcellular compartments that are arranged in specific, physiologically relevant patterns. The purple nonsulfur bacteria (PNSB) utilize a membrane-bound compartment known as the intracytoplasmic membrane (ICM) to harvest light for photosynthesis. It was previously unknown whether ICM localization within cells is systematic or irregular and if ICM localization is conserved among PNSB. Here we surveyed ICM localization in diverse PNSB and show that ICMs are spatially organized in species-specific patterns. Most strikingly, several PNSB resolutely restrict ICMs to regions near the cell poles, leaving much of the cell devoid of light-harvesting machinery. Our results demonstrate that bacteria of a common lifestyle utilize unequal portions of their intracellular space to harvest light, despite light harvesting being a process that is intuitively influenced by surface area. Our findings therefore raise fundamental questions about ICM biology and evolution.

scholarly journals A tunable multicellular timer in bacterial consortia

2020 ◽  
Author(s):  
Carlos Toscano-Ochoa ◽  
Jordi Garcia-Ojalvo
Keyword(s):  
Collective Behavior ◽  
Bacterial Population ◽  
Single Cells ◽  
Bacterial Strains ◽  
Intracellular Space ◽  
Bacterial Consortia ◽  
Robust Implementation ◽  
Time Encoding ◽  
Stationary Conditions ◽  
Molecular Components

Processing time-dependent information requires cells to quantify the durations of past regulatory events and program the time span of future signals. Such timer mechanisms are difficult to implement at the level of single cells, however, due to saturation in molecular components and stochasticity in the limited intracellular space. Multicellular implementations, on the other hand, outsource some of the components of information-processing circuits to the extracellular space, and thereby might escape those constraints. Here we develop a theoretical framework, based on a trilinear coordinate representation, to study the collective behavior of a three-strain bacterial population under stationary conditions. This framework reveals that distributing different processes (in our case the production, detection and degradation of a time-encoding signal) across distinct bacterial strains enables the robust implementation of a multicellular timer. Our analysis also shows the circuit to be easily tunable by varying the relative frequencies of the bacterial strains composing the consortium.

scholarly journals Cell chirality: its origin and roles in left–right asymmetric development

2016 ◽  
Vol 371 (1710) ◽  
pp. 20150403 ◽  
Author(s):  
Mikiko Inaki ◽  
Jingyang Liu ◽  
Kenji Matsuno
Keyword(s):  
Structural Dynamics ◽  
Cultured Cells ◽  
Mirror Image ◽  
Biological Molecules ◽  
Eukaryotic Cells ◽  
Cellular Structures ◽  
Cell Level ◽  
Whole Cell ◽  
Molecular Chirality ◽  
Left Right Asymmetry

An item is chiral if it cannot be superimposed on its mirror image. Most biological molecules are chiral. The homochirality of amino acids ensures that proteins are chiral, which is essential for their functions. Chirality also occurs at the whole-cell level, which was first studied mostly in ciliates, single-celled protozoans. Ciliates show chirality in their cortical structures, which is not determined by genetics, but by ‘cortical inheritance’. These studies suggested that molecular chirality directs whole-cell chirality. Intriguingly, chirality in cellular structures and functions is also found in metazoans. In Drosophila , intrinsic cell chirality is observed in various left–right (LR) asymmetric tissues, and appears to be responsible for their LR asymmetric morphogenesis. In other invertebrates, such as snails and Caenorhabditis elegans , blastomere chirality is responsible for subsequent LR asymmetric development. Various cultured cells of vertebrates also show intrinsic chirality in their cellular behaviours and intracellular structural dynamics. Thus, cell chirality may be a general property of eukaryotic cells. In Drosophila , cell chirality drives the LR asymmetric development of individual organs, without establishing the LR axis of the whole embryo. Considering that organ-intrinsic LR asymmetry is also reported in vertebrates, this mechanism may contribute to LR asymmetric development across phyla. This article is part of the themed issue ‘Provocative questions in left–right asymmetry’.

scholarly journals Prototypic SNARE proteins are encoded in the genomes of Heimdallarchaeota, potentially bridging the gap between the prokaryotes and eukaryotes

2019 ◽  
Author(s):  
Emilie Neveu ◽  
Dany Khalifeh ◽  
Nicolas Salamin ◽  
Dirk Fasshauer
Keyword(s):  
Gene Transfer ◽  
Eukaryotic Cell ◽  
Snare Proteins ◽  
Eukaryotic Cells ◽  
Endomembrane System ◽  
Intracellular Space ◽  
Sensitive Factor ◽  
Genes Encoding ◽  
Membrane Bound ◽  
Material Exchange

AbstractA defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together1–3. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade4,5, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.

Direct protein delivery into intact plant cells using polyhistidine peptides

2021 ◽  
Author(s):  
Yoshino Tanaka ◽  
Yoshihiko Nanasato ◽  
Kousei Omura ◽  
Keita Endoh ◽  
Tsuyoshi Kawano ◽  
...  
Keyword(s):  
Cell Lines ◽  
Fusion Proteins ◽  
Protein Delivery ◽  
Fluorescent Protein ◽  
Cultured Cells ◽  
Plant Cells ◽  
Adenosine Monophosphate ◽  
Cell Penetrating Peptides ◽  
Intracellular Space ◽  
Intracellular Fluorescence

Abstract Polyhistidine peptides (PHPs), sequences comprising only histidine residues (>His8), are effective cell-penetrating peptides for plant cells. Using PHP-fusion proteins, we aimed to deliver proteins into cultured plant cells from Nicotiana tabacum, Oryza sativa, and Cryptomeria japonica. Co-cultivation of cultured cells with fusion proteins combining maltose-binding protein (MBP), red fluorescent protein (RFP), and various PHPs (MBP-RFP-His8–His20) in one polypeptide showed the cellular uptake of fusion proteins in all plant cell lines. Maximum intracellular fluorescence was shown in MBP-RFP-His20. Further, adenylate cyclase (CyaA), a synthase of cyclic adenosine monophosphate (cAMP) activated by cytosolic calmodulin, was used as a reporter for protein delivery in living cells. A fusion protein combining MBP, RFP, CyaA, and His20 (MBP-RFP-CyaA-His20) was delivered into plant cells and increased intracellular fluorescence and cAMP production in all cell lines. The present study demonstrates that PHPs are effective carriers of proteins into the intracellular space of various cultured plant cells.

scholarly journals Mitochondrial Protein Network: From Biogenesis to Bioenergetics in Health and Disease

2020 ◽  
Vol 22 (1) ◽  
pp. 1
Author(s):  
Alessandra Ferramosca
Keyword(s):  
Crucial Role ◽  
Mitochondrial Protein ◽  
Protein Network ◽  
Eukaryotic Cells ◽  
Double Membrane ◽  
Health And Disease ◽  
Membrane Bound

Mitochondria are double membrane-bound organelles which are essential for the viability of eukaryotic cells, because they play a crucial role in bioenergetics, metabolism and signaling [...]

scholarly journals Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zev N. Kronenberg ◽  
Arang Rhie ◽  
Sergey Koren ◽  
Gregory T. Concepcion ◽  
Paul Peluso ◽  
...  
Keyword(s):  
Zebra Finch ◽  
Cultured Cells ◽  
De Novo ◽  
Single Cells ◽  
Variant Calling ◽  
Chromatin Interaction ◽  
Extended Haplotype ◽  
Benchmark Datasets ◽  
And Performance ◽  
Genome Assemblies

AbstractHaplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80–91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.

The 3D Genome Structure of Single Cells

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Tianming Zhou ◽  
Ruochi Zhang ◽  
Jian Ma
Keyword(s):  
Single Cell ◽  
Data Science ◽  
Spatial Organization ◽  
Method Development ◽  
Single Cells ◽  
Genome Structure ◽  
Computational Method ◽  
Publication Date ◽  
3D Genome ◽  
Genome Features

The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution. Here, we review recent developments in computational approaches to the analysis of scHi-C, including data processing, dimensionality reduction, imputation for enhancing data quality, and the revealing of 3D genome features at single-cell resolution. While much progress has been made in computational method development to analyze single-cell 3D genomes, substantial future work is needed to improve data interpretation and multimodal data integration, which are critical to reveal fundamental connections between genome structure and function among heterogeneous cell populations in various biological contexts. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 4 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Primary culture of secretagogue-responsive parietal cells from rabbit gastric mucosa

1989 ◽  
Vol 256 (1) ◽  
pp. G254-G263 ◽  
Author(s):  
C. S. Chew ◽  
M. Ljungstrom ◽  
A. Smolka ◽  
M. R. Brown
Keyword(s):  
Gastric Mucosa ◽  
Primary Culture ◽  
Cultured Cells ◽  
Single Cells ◽  
Parietal Cells ◽  
Ultrastructural Changes ◽  
Long Term Effects ◽  
H2 Receptor Antagonist ◽  
Morphological Transformations

A new procedure for isolation and primary culture of gastric parietal cells is described. Parietal cells from rabbit gastric mucosa are enriched to greater than 95% purity by combining a Nycodenz gradient separation with centrifugal elutriation. Cells are plated on the basement membrane matrix, Matrigel, and maintained in culture for at least 1 wk. Parietal cells cultured in this manner remain differentiated, cross-react with monoclonal H+-K+-ATPase antibodies, and respond to histamine, gastrin, and cholinergic stimulation with increased acid production as measured by accumulation of the weak base, [14C]aminopyrine. When stimulated, cultured cells undergo ultrastructural changes in which intracellular canaliculi expand and numerous microvilli are observed. These ultrastructural changes are similar to those previously found to occur in vivo and in acutely isolated parietal cells. Morphological transformations in living cells can also be observed with differential interference contrast optics in the light microscope. After histamine stimulation, intracellular canaliculi gradually expand to form large vacuolar spaces. When the H2 receptor antagonist, cimetidine, is added to histamine-stimulated cells, these vacuoles gradually disappear. The ability to maintain hormonally responsive parietal cells in primary culture should make it possible to study direct, long-term effects of a variety of agonists and antagonists on parietal cell secretory-related activity. These cultured cells should also prove to be useful for the study of calcium transients, ion fluxes, and intracellular pH as related to acid secretion in single cells, particularly since morphological transformations can be used to monitor "physiological" responses at the same time within the same cell.

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