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At least 1,243 records · Page 69Linked to original sources

C-terminal eYFP fusion impairs Escherichia coli MinE function

The Escherichia coli Min system plays an important role in the proper placement of the septum ring (Z-ring) at mid-cell during cell division. MinE forms a pole-to-pole spatial oscillator together with the membrane-bound ATPase MinD, which results in MinD having a concentration gradient with maxima at the poles and minimum at mid-cell. MinC, the direct inhibitor of the Z-ring initiator protein FtsZ, forms a complex with MinD at the membrane, thus mirroring MinD polar gradients. Therefore, MinC-mediated FtsZ inhibition occurs away from mid-cell. The existence of the oscillations was revealed by performing time-lapse microscopy with fluorescently-labeled Min proteins. These fusion proteins have been since then widely used to study properties of the Min system. Here we show that, despite permitting oscillations to occur in a range of protein concentrations, the enhanced yellow fluorescent protein (eYFP) C-terminally fused to MinE impairs its function. Combining in vivo, in vitro and in silico approaches, we demonstrate that the eYFP compromises MinE ability to displace MinC from MinD, to stimulate MinD ATPase activity and to directly bind to the membrane. Moreover, we reveal that MinE-eYFP is prone to aggregation. Taken together, our results indicate that this fusion is functionally impaired and should be used with caution in cell biological studies.

microbiology↗

JNK signaling controls branching, nucleokinesis, and positioning of centrosomes and primary cilia in migrating cortical interneurons

Aberrant migration of inhibitory interneurons can alter the formation of cortical circuitry and lead to severe neurological disorders including epilepsy, autism, and schizophrenia. However, mechanisms involved in directing the migration of these cells remain incompletely understood. In the current study, we used live-cell confocal microscopy to explore the mechanisms by which the c-Jun NH2-terminal kinase (JNK) pathway coordinates leading process branching and nucleokinesis, two cell biological processes that are essential for the guided migration of cortical interneurons. Pharmacological inhibition of JNK signaling disrupts the kinetics of leading process branching, rate and amplitude of nucleokinesis, and leads to the rearward mislocalization of the centrosome and primary cilium to the trailing process. Genetic loss of Jnk from interneurons corroborates our pharmacological observations and suggests that important mechanics of interneuron migration depend on the intrinsic activity of JNK. These findings suggest that JNK signaling regulates leading process branching, nucleokinesis, and the trafficking of centrosomes and cilia during interneuron migration, and further implicates JNK signaling as an important mediator of cortical development. Summary StatementLoss of JNK signaling reduces growth cone branching frequency, limits interstitial side branch duration, alters rate and amplitude of nucleokinesis, and mislocalizes centrosomes and primary cilia in migrating cortical interneurons.

neuroscience↗

Unfolded protein response and scaffold independent pheromone MAP kinase signalling control Verticillium dahliae growth, development and plant pathogenesis

O_LIDevelopment and virulence of the vascular plant pathogen Verticillium dahliae are connected and depend on a complex interplay between the unfolded protein response, a Ham5 independent pheromone MAP kinase module and formation of precursors for oxylipin signal molecules. C_LIO_LIGenes coding for the unfolded protein response regulator Hac1, the Ham5 MAPK scaffold protein, and the oleate {Delta}12-fatty acid desaturase Ode1 were deleted and their functions in growth, differentiation, and virulence on plants were studied using genetic, cell biology, and plant infection experiments. C_LIO_LIThe unfolded protein response transcription factor Hac1 is required for initial root colonization, fungal conidiation and propagation inside the host and is essential for resting structure formation. Microsclerotia development, growth and virulence require the pheromone response MAPK pathway, but without the Ham5 scaffold function. Single ER-associated enzymes for linoleic acid production make important contributions to fungal growth but have only a minor impact on the pathogenicity of V. dahliae. C_LIO_LIFungal growth, sporulation, dormant structure formation and plant infection require a network of the Hac1-regulated unfolded protein response, a scaffold-independent pheromone response MAPK pathway and formation of precursors for signalling. This network includes interesting targets for disease management of the vascular pathogen V. dahliae. C_LI

genetics↗

Cell cycle-associated expression patterns predict gene function in mycobacteria

While the major events in prokaryotic cell cycle progression are likely to be coordinated with transcriptional and metabolic changes, these processes remain poorly characterized. Unlike many rapidly-growing bacteria, DNA replication and cell division are temporally-resolved in mycobacteria, making these slow-growing organisms a potentially useful system to investigate the prokaryotic cell cycle. To determine if cell-cycle dependent gene regulation occurs in mycobacteria, we characterized the temporal changes in the transcriptome of synchronously replicating populations of Mycobacterium tuberculosis (Mtb). By enriching for genes that display a sinusoidal expression pattern, we discover 485 genes that oscillate with a period consistent with the cell cycle. During cytokinesis, the timing of gene induction could be used to predict the timing of gene function, as mRNA abundance was found to correlate with the order in which proteins were recruited to the developing septum. Similarly, the expression pattern of primary metabolic genes could be used to predict the relative importance of these pathways for different cell cycle processes. Pyrimidine synthetic genes peaked during DNA replication and their depletion caused a filamentation phenotype that phenocopied defects in this process. In contrast, the IMP dehydrogenase guaB2 dedicated to guanosine synthesis displayed the opposite expression pattern and its depletion perturbed septation. Together, these data imply obligate coordination between primary metabolism and cell division, and identify periodically regulated genes that can be related to specific cell biological functions.

microbiology↗

Increases in ambient temperature progressively disassemble Arabidopsis phytochrome B from individual photobodies with distinct thermostabilities

Warm temperature is postulated to induce plant thermomorphogenesis through a signaling mechanism similar to shade, as both destabilize the active form of the photoreceptor and thermosensor phytochrome B (phyB). At the cellular level, shade antagonizes phyB signaling by triggering phyB disassembly from photobodies. Here we report temperature-dependent photobody localization of fluorescent protein-tagged phyB (phyB-FP) in the epidermal cells of Arabidopsis hypocotyl and cotyledon. Our results demonstrate that warm temperature operates through different photobody dynamics from shade. Increases in temperature from 12{degrees}C to 27{degrees}C incrementally reduce photobody number by stimulating phyB-FP disassembly from selective thermo-unstable photobodies. The thermostability of photobodies relies on phyBs photosensory module. Surprisingly, elevated temperatures inflict opposite effects on phyBs functions in the hypocotyl and cotyledon despite inducing similar photobody dynamics, indicative of tissue/organ-specific temperature signaling circuitry downstream of photobody dynamics. Our results thus provide direct cell biology evidence supporting an early temperature signaling mechanism via dynamic assembly/disassembly of individual photobodies possessing distinct thermostabilities.

plant biology↗

Tudor staphylococcal nuclease acts as a docking platform for stress granule components in Arabidopsis thaliana

Adaptation to stress depends on the modulation of gene expression. Regulation of mRNA stability and degradation in stress granules (SGs), - cytoplasmic membraneless organelles composed of messenger ribonucleoprotein (mRNP) complexes, - plays an important role in fine-tuning of gene expression. In addition, SG formation can modulate stress signaling pathways by protein sequestration. Molecular composition, structure, and function of SGs in plants remain obscure. Recently, we established Tudor Staphylococcal Nuclease (TSN or Tudor-SN; also known as SND1) as integral component of SGs in Arabidopsis thaliana. Here, we combined purification of TSN interactome with cell biology, reverse genetics and bioinformatics to study composition and function of SGs in plants. We found that under both normal (in the absence of stress) and stress conditions TSN interactome is enriched in the homologues of known mammalian and yeast SG proteins, in addition to novel or plant-specific SG components. We estimate that upon stress perception, approximately half of TSN interactors are recruited to SGs de novo, in a stress-dependent manner, while another half represent a dense protein-protein interaction network pre-formed before onset of stress. Almost all TSN-interacting proteins are moderately or highly disordered and approximately 20% of them are predisposed for liquid-liquid phase separation (LLPS). This suggests that plant SGs, similarly to mammalian and yeast counterparts, are multicomponent viscous liquid droplets. Finally, we have discovered that evolutionary conserved SNF1-related protein kinase 1 (SnRK1) interacts with TSN in heat-induced SGs and that SnRK1 activation critically depends on the presence of TSN and formation of SGs. Altogether, our results establish TSN as a docking platform for SG-associated proteins and important stress signal mediator in plants.

plant biology↗

Regulated control of gene therapies with a drug induced switch

To date, gene therapies for human application rely on engineered promoters that cannot be finely controlled. Here, we report a universal switch element that allows precise control for gene silencing or gene replacement after exposure to a small molecule. Importantly, these small molecule inducers are in human use, are orally bioavailable when given to animals or humans, and can reach both peripheral tissues and the brain. Moreover, the switch system (Xon) does not require the co-expression of any regulatory proteins. Using Xon, translation of desired elements for gene knockdown or gene replacement occurs after a single oral dose, and expression levels can be controlled by drug dose or in waves with repeat drug intake. This universal switch can provide temporal control of gene editing machinery and gene addition cassettes that can be adapted to cell biology applications and animal studies. Additionally, due to the oral bioavailability and safety of the drugs employed, the Xon switch provides an unprecedented opportunity to refine gene therapies for more appropriate human application.

molecular biology↗

Efficient Retroelement-Mediated DNA Writing in Bacteria

The ability to efficiently and dynamically change information stored in genomes would enable powerful strategies for studying cell biology and controlling cellular phenotypes. Current recombineering-mediated DNA writing platforms in bacteria are limited to specific laboratory conditions, often suffer from suboptimal editing efficiencies, and are not suitable for in situ applications. To overcome these limitations, we engineered a retroelement-mediated DNA writing system that enables efficient and precise editing of bacterial genomes without the requirement for target-specific elements or selection. We demonstrate that this DNA writing platform enables a broad range of applications, including efficient, scarless, and cis-element-independent editing of targeted microbial genomes within complex communities, the high-throughput mapping of spatial information and cellular interactions into DNA memory, and the continuous evolution of cellular traits. One Sentence SummaryHighly-efficient, dynamic, and conditional genome writers are engineered for DNA memory, genome engineering, editing microbial communities, high-resolution mapping of cellular connectomes, and modulating cellular evolution.

synthetic biology↗

Visualizing ultrastructural details of placental tissue with super-resolution structured illumination microscopy

Super-resolution fluorescence microscopy is a widely employed technique in cell biology research, yet remains relatively unexplored in the field of histo-pathology. Here, we describe the sample preparation steps and acquisition parameters necessary to obtain fluorescent multicolor super-resolution structured illumination microscopy (SIM) images of both formalin-fixed paraffin-embedded and cryo-preserved placental tissue sections. We compare super-resolved images of chorionic villi against diffraction-limited deconvolution microscopy and demonstrate the significant contrast and resolution enhancement attainable with SIM. We show that SIM resolves ultrastructural details such as the syncytiotrophoblasts microvilli brush border, which up until now has been only resolvable by electron microscopy.

pathology↗

Anomalous Diffusion Characterization by Fourier-Transform FRAP with Patterned Illumination

Fourier transform fluorescence recovery after photobleaching (FT-FRAP) with patterned illumination is theorized and demonstrated for quantitatively evaluating normal and anomalous diffusion. Diffusion characterization is routinely performed to assess mobility in cell biology, pharmacology, and food science. Conventional FRAP is noninvasive, has low sample volume requirements, and can rapidly measure diffusion over distances of a few micrometers. However, conventional point-bleach measurements are complicated by signal-to-noise limitations, the need for precise knowledge of the bleach beam profile, potential for bias due to sample heterogeneity, and poor compatibility with multi-photon excitation due to local heating. In FT-FRAP with patterned illumination, the time-dependent fluorescence recovery signal is concentrated to puncta in the spatial Fourier domain through patterned bleaching, with substantial improvements in signal-to-noise, mathematical simplicity, representative sampling, and multiphoton compatibility. A custom nonlinear-optical beam-scanning microscope enabled patterned illumination for photobleaching through two-photon excitation. Measurements in the spatial Fourier domain removed dependence on the bleach profile, suppressing bias from imprecise knowledge of the point spread function. For normal diffusion, the fluorescence recovery produced a simple single-exponential decay in the spatial Fourier domain, in excellent agreement with theoretical predictions. Simultaneous measurement of diffusion at multiple length scales was enabled through analysis of multiple spatial harmonics of the bleaching pattern. Anomalous diffusion was characterized by FT-FRAP through a nonlinear fit to multiple spatial harmonics of the fluorescence recovery. Constraining the fit to describe diffusion over multiple length scales resulted in higher confidence in the recovered fitting parameters. Additionally, phase analysis in FT-FRAP was shown to inform on flow/sample translation. Statement of SignificanceFourier transform fluorescence recovery after photobleaching (FT-FRAP) with patterned illumination greatly improves the accuracy of diffusion assessments and simultaneously accesses information on both normal and anomalous diffusion in a single experiment.

biophysics↗

Dynamic changes in tRNA modifications and abundance during T-cell activation

The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of T-cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observe a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode "slippery codons", that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with a HIV gag-pol frameshifting site reporter. These results may explain HIVs specific tropism towards proliferating T-Cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity. Significance statementThe tRNA pool decodes genetic information during translation. As such, it is subject to intricate physiological regulation in all species, across different physiological conditions. Here we show for the first time a program that governs the tRNA pool and its interaction with the transcriptome upon a physiological cellular proliferation- T-cells activation. We found that upon antigenic activation of T-cells, their tRNA and mRNA pools undergo coordinated and complementary changes, which are relaxed when cells reduce back their proliferation rate and differentiate into memory cells. We found a reduction in two particular tRNA modifications that have a role in governing translation fidelity and frameshift prevention. This exposes a vulnerability in activated T-cells that may be utilized by HIV for its replication. ClassificationBIOLOGICAL SCIENCES; cell biology

genomics↗

Proximity-based proteomics reveals the thylakoid lumen proteome in the cyanobacterium Synechococcus sp. PCC 7002

Cyanobacteria possess unique intracellular organization. Many proteomic studies have examined different features of cyanobacteria to learn about the structure-function relationships between the intracellular structures of cyanobacteria and their roles in cells. While these studies have made great progress in understanding cyanobacterial physiology, the previous fractionation methods used to purify cellular structures have limitations; specifically, certain regions of cells cannot be purified with existing fractionation methods. Proximity-based proteomics techniques were developed to overcome the limitations of biochemical fractionation for proteomics. Proximity-based proteomics relies on spatiotemporal protein labeling followed by mass spectrometry of the labeled proteins to determine the proteome of the region of interest. We have performed proximity-based proteomics in the cyanobacterium Synechococcus sp. PCC 7002 with the APEX2 enzyme, an engineered ascorbate peroxidase. We determined the proteome of the thylakoid lumen, a region of the cell that has remained challenging to study with existing methods, using a PsbU-APEX2 gene fusion. This study demonstrates the power of APEX2 as a tool to study the cell biology of intracellular features of cyanobacteria with enhanced spatiotemporal resolution.

biochemistry↗

The number of growing microtubules and nucleus-nucleus interactions uniquely regulate nuclear movement in Drosophila muscle

Nuclear movement is a fundamental process of eukaryotic cell biology. Skeletal muscle presents an intriguing model to study nuclear movement because its development requires the precise positioning of multiple nuclei within a single cytoplasm. Furthermore, there is a high correlation between aberrant nuclear positioning and poor muscle function. Although many genes that regulate nuclear movement have been identified, the mechanisms by which these genes act is not known. Using Drosophila melanogaster muscle development as a model system, and a combination of live-embryo microscopy and laser ablation of nuclei, we have found that phenotypically similar mutants are based in different molecular disruptions. Specifically, ensconsin (Drosophila MAP7) regulates the number of growing microtubules that are used to move nuclei whereas bocksbeutel (Drosophila emerin) and klarsicht (Drosophila KASH-protein regulate interactions between nuclei.

developmental biology↗

Xela DS2 and Xela VS2: two novel skin epithelial-like cell lines from adult African clawed frog (Xenopus laevis) and their response to an extracellular viral dsRNA analogue

The skin epithelial layer acts as an important immunological barrier against pathogens and is capable of recognizing and responding to pathogen associated molecular patterns (PAMPs) in human and mouse models. Although presumed, it is unknown whether amphibian skin epithelial cells exhibit the ability to respond to PAMPs such as viral double-stranded RNA (dsRNA). To address this, two cell lines from the dorsal skin (Xela DS2) and ventral skin (Xela VS2) of the African clawed frog (Xenopus laevis) were established. Xela DS2 and Xela VS2 cells have an epithelial-like morphology, express genes associated with epithelial cells, and lack senescence-associated beta-galactosidase activity. Cells grow optimally in 70% Leibovitz’s L-15 medium supplemented with 15% fetal bovine serum at 26°C. Upon treatment with poly(I:C), a synthetic viral dsRNA analogue and known type I interferon inducer, Xela DS2 and Xela VS2 exhibit marked upregulation of key pro-inflammatory and antiviral transcripts suggesting frog epithelial cells participate in the recognition of extracellular viral dsRNA and production of local inflammatory signals; similar to human and mouse models. Currently, these are the only known Xenopus laevis skin epithelial-like cell lines and will be important for future research in amphibian epithelial cell biology, initial host-pathogen interactions, and rapid screening of the effects of environmental stressors, including contaminants, on frog skin epithelial cells.Competing Interest StatementThe authors have declared no competing interest.View Full Text

zoology↗

CytofRUV: Removing unwanted variation to integrate multiple CyTOF datasets

Mass cytometry (CyTOF) is a technology that has revolutionised single cell biology. One illuminating application of CyTOF has been in understanding the mechanisms of blood cancer resistance to therapy. Longitudinal studies of clinical cohorts during drug treatment provide a deeper understanding of the molecular changes that underlie sensitivity or resistance to treatment in each patient. However, understanding the biological impact of a cancer drug in such studies necessitates the integration of multiple CyTOF batches. To date, the integration of CyTOF datasets remains a challenge due to technical differences arising in multiple batches. To overcome this limitation, we developed an approach called CytofRUV for analysing multiple CyTOF batches which includes an R-Shiny application with diagnostics plots. CytofRUV can correct for batch effects and integrate data from large numbers of patients and conditions across batches, to confidently compare cellular changes and correlate these with clinically relevant outcomes.

bioinformatics↗

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

Ascomycota, the largest and best-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts); organisms from all three subphyla have been invaluable as models in diverse fields (e.g., biotechnology, cell biology, genetics, and medicine). Despite its importance, we still lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. To address these gaps, we examined 1,107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species to infer the Ascomycota phylogeny, estimate its timetree, and examine the evolution of key genomic properties. We inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran (~563 {+/-} 68 million years ago). Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina, the two taxon-rich subphyla, differed greatly in their genome properties. Saccharomycotina typically have smaller genomes, lower GC contents, lower numbers of genes, and higher rates of molecular sequence evolution compared to Pezizomycotina. Ancestral state reconstruction showed that the genome properties of the Saccharomycotina and Pezizomycotina last common ancestors were very similar, enabling inference of the direction of evolutionary change. For example, we found that a lineage-specific acceleration led to a 1.6-fold higher evolutionary rate in Saccharomycotina, whereas the 10% difference in GC content between Saccharomycotina and Pezizomycotina genomes stems from a trend toward AT bases within budding yeasts and toward GC bases within filamentous fungi. These results provide a robust evolutionary framework for understanding the diversification of the largest fungal phylum.

evolutionary biology↗

A vector system for fast-forward in vivo studies of the ZAR1 resistosome in the model plant Nicotiana benthamiana

Nicotiana benthamiana has emerged as a complementary experimental system to Arabidopsis. It enables fast-forward in vivo analyses primarily through transient gene expression and is particularly popular in the study of plant immunity. Recently, our understanding of NLR plant immune receptors has greatly advanced following the discovery of Arabidopsis ZAR1 resistosome. Here, we describe a novel vector system of 52 plasmids that enables functional studies of the ZAR1 resistosome in N. benthamiana. We showed that ZAR1 stands out among the coiled coil class of NLRs for being highly conserved across distantly related dicot plant species and confirmed NbZAR1 as the N. benthamiana ortholog of Arabidopsis ZAR1. NbZAR1 triggers autoimmune cell death in N. benthamiana and this activity is dependent on a functional N-terminal 1 helix. C-terminally tagged NbZAR1 remains functional in N. benthamiana thus enabling cell biology and biochemical studies in this plant system. We conclude that the NbZAR1 open source plasmids form an additional experimental system to Arabidopsis for in planta resistosome studies.

plant biology↗

Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli

Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation via the Calvin cycle. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an engineered E. coli strain. Expression of 20 CCM genes enabled E. coli to grow by fixing CO2 from ambient air into biomass, with growth depending on CCM components. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, thereby laying the groundwork for deeper study and engineering of the cell biology supporting CO2 assimilation in diverse organisms.One Sentence Summary A bacterial CO2 concentrating mechanism enables E. coli to fix CO2 from ambient air.Competing Interest StatementD.F.S. is a co-founder of Scribe Therapeutics and a scientific advisory board member of Scribe Therapeutics and Mammoth Biosciences. A.B.-E. is co-founder of b.fab. These companies were not involved in this research in any way. All other authors declare no competing interests.View Full Text

synthetic biology↗