Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signaling
(Source: EMBO Journal)
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Qiu, R., DeRocco, V. C., Harris, C., Sharma, A., Hingorani, M. M., Erie, D. A., Weninger, K. R. Tags: Corrigendum Source Type: research
Cas9 slide-and-seek for phage defense and genome engineering
How does the Cas9 nuclease locate a specific 20-nucleotide target sequence in a crowded intracellular environment packed with mega bases of distracting non-target DNA? Previously, it was shown that Cas9 finds DNA targets via three-dimensional diffusion. In this issue of The EMBO Journal, Globyte et al (2019) reveal another dimension of the search process, which involves short-range one-dimensional sliding. These results have implications for understanding the natural function of Cas9 and its applications in genome engineering experiments. (Source: EMBO Journal)
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Santiago-Frangos, A., Wiegand, T., Wiedenheft, B. Tags: DNA Replication, Repair & Recombination, Methods & Resources News [amp ] Views Source Type: research
The nature of the biological material and the irreproducibility problem in biomedical research
Biomedical research has a reproducibility problem since various crucial landmark papers could not be independently reproduced. While there are many causes related to statistical analysis, methodology or insufficient reporting of experimental details, this commentary argues that the complexity of biological material itself is, until now, a largely ignored source of irreproducibility. By discussing examples from evolutionary biology, intrinsically disordered proteins and current biomedical research, it contends that some results are irreproducible because we do not have the knowledge, the tools or the analytical ability to u...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Papamokos, G. V. Tags: Commentary Source Type: research
A dual role for cell plate-associated PI4K{beta} in endocytosis and phragmoplast dynamics during plant somatic cytokinesis
Plant cytokinesis involves membrane trafficking and cytoskeletal rearrangements. Here, we report that the phosphoinositide kinases PI4Kβ1 and PI4Kβ2 integrate these processes in Arabidopsis thaliana (Arabidopsis) roots. Cytokinetic defects of an Arabidopsis pi4kβ1 pi4kβ2 double mutant are accompanied by defects in membrane trafficking. Specifically, we show that trafficking of the proteins KNOLLE and PIN2 at the cell plate, clathrin recruitment, and endocytosis is impaired in pi4kβ1 pi4kβ2 double mutants, accompanied by unfused vesicles at the nascent cell plate and around cell wall stubs. Int...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Lin, F., Krishnamoorthy, P., Schubert, V., Hause, G., Heilmann, M., Heilmann, I. Tags: Membrane & Intracellular Transport, Plant Biology Articles Source Type: research
Long-term expanding human airway organoids for disease modeling
Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here, we describe a method to establish long-term-expanding human airway organoids from broncho-alveolar resections or lavage material. The pseudostratified airway organoids consist of basal cells, functional multi-ciliated cells, mucus-producing secretory cells, and CC10-secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR function in an organoid swelling assay. Organoids established from lung cancer resections and metastasis biopsies r...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Sachs, N., Papaspyropoulos, A., Zomer-van Ommen, D. D., Heo, I., Böttinger, L., Klay, D., Weeber, F., Huelsz-Prince, G., Iakobachvili, N., Amatngalim, G. D., de Ligt, J., van Hoeck, A., Proost, N., Viveen, M. C., Lyubimova, A., Teeven, L., Derakhs Tags: Cancer, Methods & Resources, Molecular Biology of Disease Source Type: research
CDK phosphorylation of Xenopus laevis M18BP1 promotes its metaphase centromere localization
Chromosome segregation requires the centromere, the site on chromosomes where kinetochores assemble in mitosis to attach chromosomes to the mitotic spindle. Centromere identity is defined epigenetically by the presence of nucleosomes containing the histone H3 variant CENP-A. New CENP-A nucleosome assembly occurs at the centromere every cell cycle during G1, but how CENP-A nucleosome assembly is spatially and temporally restricted remains poorly understood. Centromere recruitment of factors required for CENP-A assembly is mediated in part by the three-protein Mis18 complex (Mis18α, Mis18β, M18BP1). Here, we show ...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: French, B. T., Straight, A. F. Tags: Cell Cycle, Chromatin, Epigenetics, Genomics & Functional Genomics Articles Source Type: research
Atoh1+ secretory progenitors possess renewal capacity independent of Lgr5+ cells during colonic regeneration
During homeostasis, the colonic epithelium is replenished every 3–5 days by rapidly cycling Lgr5+ stem cells. However, various insults can lead to depletion of Lgr5+ stem cells, and colonic epithelium can be regenerated from Lgr5-negative cells. While studies in the small intestine have addressed the lineage identity of the Lgr5-negative regenerative cell population, in the colon this question has remained unanswered. Here, we set out to identify which cell(s) contribute to colonic regeneration by performing genetic fate-mapping studies of progenitor populations in mice. First, using keratin-19 (Krt19) to mark a...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Castillo-Azofeifa, D., Fazio, E. N., Nattiv, R., Good, H. J., Wald, T., Pest, M. A., de Sauvage, F. J., Klein, O. D., Asfaha, S. Tags: Development & Differentiation, Molecular Biology of Disease, Stem Cells Articles Source Type: research
Bacterial killing by complement requires membrane attack complex formation via surface-bound C5 convertases
The immune system kills bacteria by the formation of lytic membrane attack complexes (MACs), triggered when complement enzymes cleave C5. At present, it is not understood how the MAC perturbs the composite cell envelope of Gram-negative bacteria. Here, we show that the role of C5 convertase enzymes in MAC assembly extends beyond the cleavage of C5 into the MAC precursor C5b. Although purified MAC complexes generated from preassembled C5b6 perforate artificial lipid membranes and mammalian cells, these components lack bactericidal activity. In order to permeabilize both the bacterial outer and inner membrane and thus kill a...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Heesterbeek, D. A., Bardoel, B. W., Parsons, E. S., Bennett, I., Ruyken, M., Doorduijn, D. J., Gorham, R. D., Berends, E. T., Pyne, A. L., Hoogenboom, B. W., Rooijakkers, S. H. Tags: Membrane & Intracellular Transport, Microbiology, Virology & Host Pathogen Interaction Articles Source Type: research
The pseudokinase TRIB1 toggles an intramolecular switch to regulate COP1 nuclear export
COP1 is a highly conserved ubiquitin ligase that regulates diverse cellular processes in plants and metazoans. Tribbles pseudokinases, which only exist in metazoans, act as scaffolds that interact with COP1 and its substrates to facilitate ubiquitination. Here, we report that, in addition to this scaffolding role, TRIB1 promotes nuclear localization of COP1 by disrupting an intramolecular interaction between the WD40 domain and a previously uncharacterized regulatory site within COP1. This site, which we have termed the pseudosubstrate latch (PSL), resembles the consensus COP1-binding motif present in known COP1 substrates...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Kung, J. E., Jura, N. Tags: Membrane & Intracellular Transport, Post-translational Modifications, Proteolysis & Proteomics Articles Source Type: research
CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion
The Streptococcus pyogenes CRISPR/Cas9 (SpCas9) nuclease has been widely applied in genetic engineering. Despite its importance in genome editing, aspects of the precise molecular mechanism of Cas9 activity remain ambiguous. In particular, because of the lack of a method with high spatio-temporal resolution, transient interactions between Cas9 and DNA could not be reliably investigated. It therefore remains controversial how Cas9 searches for protospacer adjacent motif (PAM) sequences. We have developed single-molecule Förster resonance energy transfer (smFRET) assays to monitor transient interactions of Cas9 and D...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Globyte, V., Lee, S. H., Bae, T., Kim, J.-S., Joo, C. Tags: DNA Replication, Repair & Recombination, Methods & Resources Articles Source Type: research
Beclin1-driven autophagy modulates the inflammatory response of microglia via NLRP3
Alzheimer's disease is characterized not only by extracellular amyloid plaques and neurofibrillary tangles, but also by microglia-mediated neuroinflammation. Recently, autophagy has been linked to the regulation of the inflammatory response. Thus, we investigated how an impairment of autophagy mediated by BECN1/Beclin1 reduction, as described in Alzheimer's disease patients, would influence cytokine production of microglia. Acutely stimulated microglia from Becn1+/– mice exhibited increased expression of IL-1beta and IL-18 compared to wild-type microglia. Becn1+/–APPPS1 mice also contained enhanced IL-1beta lev...
Source: EMBO Journal - February 15, 2019 Category: Molecular Biology Authors: Houtman, J., Freitag, K., Gimber, N., Schmoranzer, J., Heppner, F. L., Jendrach, M. Tags: Immunology, Neuroscience Articles Source Type: research
Selective inhibition of the Fc{varepsilon}RI-induced de novo synthesis of mediators by an inhibitory receptor
(Source: EMBO Journal)
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Abramson, J., Licht, A., Pecht, I. Tags: Corrigendum Source Type: research
Nonsense shielding: protecting RNA from decay leads to cancer
Despite intense scrutiny, the signals that determine whether a given RNA is degraded by the highly conserved and selective nonsense-mediated RNA decay (NMD) pathway remain murky. In this issue of The EMBO Journal, Kishor et al shed light on this issue by demonstrating that the RNA-binding protein, hnRNP L, protects a subset of RNAs from degradation by NMD. This mechanism is responsible for stabilizing the mRNA encoding the pro-survival "oncogenic" protein, BCL-2, in B-cell lymphoma. (Source: EMBO Journal)
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Wilkinson, M. F., Cook-Andersen, H. Tags: Cancer, RNA Biology News [amp ] Views Source Type: research
Revealing the Superpowers of PrimPol: rescuing replicating microsatellites
R-loops are potentially mutagenic three-stranded structures where RNA has hybridized to one strand of DNA and displaced the other, exposing ssDNA. Long repeated R-loop-forming sequences are known to cause genomic instability and are associated with disease. Šviković et al (2019) show that even short tandem (microsatellite) repeats, abundant in the vertebrate genome, do form R-loops and present a barrier to replication. However, the replication fork can move past these short R-loop-forming repeats through the re-priming action of primase–polymerase (PrimPol), thus avoiding the loss of epigenetic inf...
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Reid, J. E., Fischer, T. Tags: DNA Replication, Repair & Recombination News [amp ] Views Source Type: research
Getting into shape: tissue tension drives oriented cell divisions during organogenesis
The shapes and architecture of the organs in the animal body develop through complex coordination of cell shape change, cell migration, and cell proliferation. Finegan et al (2019) use the simple model of the Drosophila ovary and elongation of each egg chamber to explore this process. They find that a gradient of myosin-driven tension exists along the axis of organ elongation and that this orients the division of the constituent cells. This and other recent work highlight how tissue-level tension plays a key role in regulating tissue architecture. (Source: EMBO Journal)
Source: EMBO Journal - February 1, 2019 Category: Molecular Biology Authors: Manning, L. A., Peifer, M. Tags: Cell Adhesion, Polarity & Cytoskeleton, Development & Differentiation News [amp ] Views Source Type: research
