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  • 1.
    Devarenne, Tim, P.
    et al.
    BTI, Cornell University, USA.
    Ekengren, Sophia K.
    BTI, Cornell University, USA.
    Pedley, K. F.
    BTI, Cornell University, USA.
    Martin, Gregory, B.
    BTI, Cornell University.
    Adi3 is a Pdk1-interacting AGC kinase that negatively regulates plant cell death2006In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 25, no 1, p. 255-265Article in journal (Refereed)
    Abstract [en]

    Bacterial speck disease in tomato is caused by Pseudomonas syringae pv. tomato. Resistance to this disease is conferred by the host Pto kinase, which recognizes P. s. pv. tomato strains that express the effector AvrPto. We report here that an AvrPto-dependent Pto-interacting protein 3 (Adi3) is a member of the AGC family of protein kinases. In mammals, AGC kinases are regulated by 3-phosphoinositide-dependent protein kinase-1 (Pdk1). We characterized tomato Pdk1 and showed that Pdk1 and Pto phosphorylate Adi3. Gene silencing of Adi3 in tomato causes MAPKKK alpha-dependent formation of necrotic lesions. Use of a chemical inhibitor of Pdk1, OSU-03012, also implicates Pdk1 and Adi3 in plant cell death regulation. Adi3 thus appears to function analogously to the mammalian AGC kinase protein kinase B/Akt by negatively regulating cell death via Pdk1 phosphorylation. We speculate that the negative regulatory function of Adi3 might be subverted by interaction with Pto/AvrPto, leading to host cell death that is associated with pathogen attack.

  • 2. Jakobsen, Lis
    et al.
    Vanselow, Katja
    Skogs, Marie
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Toyoda, Yusuke
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Poser, Ina
    Falkenby, Lasse G.
    Bennetzen, Martin
    Westendorf, Jens
    Nigg, Erich A.
    Uhlen, Mathias
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).
    Hyman, Anthony A.
    Andersen, Jens S.
    Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods2011In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 30, no 8, p. 1520-1535Article in journal (Refereed)
    Abstract [en]

    Centrosomes in animal cells are dynamic organelles with a proteinaceous matrix of pericentriolar material assembled around a pair of centrioles. They organize the microtubule cytoskeleton and the mitotic spindle apparatus. Mature centrioles are essential for biogenesis of primary cilia that mediate key signalling events. Despite recent advances, the molecular basis for the plethora of processes coordinated by centrosomes is not fully understood. We have combined protein identification and localization, using PCP-SILAC mass spectrometry, BAC transgeneOmics, and antibodies to define the constituents of human centrosomes. From a background of non-specific proteins, we distinguished 126 known and 40 candidate centrosomal proteins, of which 22 were confirmed as novel components. An antibody screen covering 4000 genes revealed an additional 113 candidates. We illustrate the power of our methods by identifying a novel set of five proteins preferentially associated with mother or daughter centrioles, comprising genes implicated in cell polarity. Pulsed labelling demonstrates a remarkable variation in the stability of centrosomal protein complexes. These spatiotemporal proteomics data provide leads to the further functional characterization of centrosomal proteins.

  • 3. Moolenaar, G. F.
    et al.
    Goosen, N.
    Clue to damage recognition by UvrB: residues in the beta-hairpin structure prevent binding to non-damaged DNA2001In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 20, no 21, p. 6140-6149Article in journal (Refereed)
    Abstract [en]

    UvrB, the ultimate damage-recognizing component of bacterial nucleotide excision repair, contains a flexible beta -hairpin rich in hydrophobic residues. We describe the properties of UvrB mutants in which these residues have been mutated. The results show that Y101 and F108 in the tip of the hairpin are important for the strand-separating activity of UvrB, supporting the model that the beta -hairpin inserts between the two DNA strands during the search for DNA damage. Residues Y95 and Y96 at the base of the hairpin have a direct role in damage recognition and are positioned close to the damage in the UvrB-DNA complex. Strikingly, substituting Y92 and Y93 results in a protein that is lethal to the cell. The mutant protein forms pre- incision complexes on non-damaged DNA, indicating that Y92 and Y93 function in damage recognition by preventing UvrB binding to non-damaged sites. We propose a model for damage recognition by UvrB in which, stabilized by the four tyrosines at the base of the hairpin, the damaged nucleotide is flipped out of the DNA helix.

  • 4. Richter, Katharina N.
    et al.
    Revelo, Natalia H.
    Seitz, Katharina J.
    Helm, Martin S.
    Sarkar, Deblina
    Saleeb, Rebecca S.
    D'Este, Elisa
    Eberle, Jessica
    Wagner, Eva
    Vogl, Christian
    Lazaro, Diana F.
    Richter, Frank
    Coy-Vergara, Javier
    Coceano, Giovanna
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Boyden, Edward S.
    Duncan, Rory R.
    Hell, Stefan W.
    Lauterbach, Marcel A.
    Lehnart, Stephan E.
    Moser, Tobias
    Outeiro, Tiago F.
    Rehling, Peter
    Schwappach, Blanche
    Testa, Ilaria
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zapiec, Bolek
    Rizzoli, Silvio O.
    Glyoxal as an alternative fixative to formaldehyde in immunostaining and super-resolution microscopy2018In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 37, no 1, p. 139-159Article in journal (Refereed)
    Abstract [en]

    Paraformaldehyde (PFA) is the most commonly used fixative for immunostaining of cells, but has been associated with various problems, ranging from loss of antigenicity to changes in morphology during fixation. We show here that the small dialdehyde glyoxal can successfully replace PFA. Despite being less toxic than PFA, and, as most aldehydes, likely usable as a fixative, glyoxal has not yet been systematically tried in modern fluorescence microscopy. Here, we tested and optimized glyoxal fixation and surprisingly found it to be more efficient than PFA-based protocols. Glyoxal acted faster than PFA, cross-linked proteins more effectively, and improved the preservation of cellular morphology. We validated glyoxal fixation in multiple laboratories against different PFA-based protocols and confirmed that it enabled better immunostainings for a majority of the targets. Our data therefore support that glyoxal can be a valuable alternative to PFA for immunostaining.

  • 5. Romanov, Roman A.
    et al.
    Alpar, Alan
    Zhang, Ming-Dong
    Zeisel, Amit
    Calas, Andre
    Landry, Marc
    Fuszard, Matthew
    Shirran, Sally L.
    Schnell, Robert
    Dobolyi, Arpad
    Olah, Mark
    Spence, Lauren
    Mulder, Jan
    Martens, Henrik
    Palkovits, Miklos
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sitte, Harald H.
    Botting, Catherine H.
    Wagner, Ludwig
    Linnarsson, Sten
    Hökfelt, Tomas
    Harkany, Tibor
    A secretagogin locus of the mammalian hypothalamus controls stress hormone release2015In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 34, no 1, p. 36-54Article in journal (Refereed)
    Abstract [en]

    A hierarchical hormonal cascade along the hypothalamic-pituitary-adrenal axis orchestrates bodily responses to stress. Although corticotropin-releasing hormone (CRH), produced by parvocellular neurons of the hypothalamic paraventricular nucleus (PVN) and released into the portal circulation at the median eminence, is known to prime downstream hormone release, the molecular mechanism regulating phasic CRH release remains poorly understood. Here, we find a cohort of parvocellular cells interspersed with magnocellular PVN neurons expressing secretagogin. Single-cell transcriptome analysis combined with protein interactome profiling identifies secretagogin neurons as a distinct CRH-releasing neuron population reliant on secretagogin's Ca2+ sensor properties and protein interactions with the vesicular traffic and exocytosis release machineries to liberate this key hypothalamic releasing hormone. Pharmacological tools combined with RNA interference demonstrate that secretagogin's loss of function occludes adrenocorticotropic hormone release from the pituitary and lowers peripheral corticosterone levels in response to acute stress. Cumulatively, these data define a novel secretagogin neuronal locus and molecular axis underpinning stress responsiveness.

  • 6. von Eyss, Björn
    et al.
    Maaskola, Jonas
    Memczak, Sebastian
    Möllmann, Katharina
    Schuetz, Anja
    Loddenkemper, Christoph
    Tanh, Mai-Dinh
    Otto, Albrecht
    Muegge, Kathrin
    Heinemann, Udo
    Rajewsky, Nikolaus
    Ziebold, Ulrike
    The SNF2-like helicase HELLS mediates E2F3-dependent transcription and cellular transformation.2012In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 31, no 4, p. 972-985Article in journal (Refereed)
    Abstract [en]

    The activating E2F-transcription factors are best known for their dependence on the Retinoblastoma protein and their role in cellular proliferation. E2F3 is uniquely amplified in specific human tumours where its expression is inversely correlated with the survival of patients. Here, E2F3B interaction partners were identified by mass spectrometric analysis. We show that the SNF2-like helicase HELLS interacts with E2F3A in vivo and cooperates with its oncogenic functions. Depletion of HELLS severely perturbs the induction of E2F-target genes, hinders cell-cycle re-entry and growth. Using chromatin immmunoprecipitation coupled to sequencing, we identified genome-wide targets of HELLS and E2F3A/B. HELLS binds promoters of active genes, including the trithorax-related MLL1, and co-regulates E2F3-dependent genes. Strikingly, just as E2F3, HELLS is overexpressed in human tumours including prostate cancer, indicating that either factor may contribute to the malignant progression of tumours. Our work reveals that HELLS is important for E2F3 in tumour cell proliferation.

  • 7. Wu, S.R.
    et al.
    Sjöberg, M.
    Wallin, M.
    Lindqvist, B.
    Hebert, Hans
    Department of Biosciences and Nutrition, Karolinska Institute.
    Koeck, Philip J. B.
    Garoff, H.
    Turning of the receptor binding domains opens up the murine leukaemia virus Env for membrane fusion2008In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 27, no 20, p. 2799-2808Article in journal (Refereed)
    Abstract [en]

    The activity of the membrane fusion protein Env of Moloney mouse leukaemia virus is controlled by isomerization of the disulphide that couples its transmembrane (TM) and surface (SU) subunits. We have arrested Env activation at a stage prior to isomerization by alkylating the active thiol in SU and compared the structure of isomerization-arrested Env with that of native Env. Env trimers of respective form were isolated from solubilized particles by sedimentation and their structures were reconstructed from electron microscopic images of both vitrified and negatively stained samples. We found that the protomeric unit of both trimers formed three protrusions, a top, middle and a lower one. The atomic structure of the receptor-binding domain of SU fitted into the upper protrusion. This was formed similar to a bent finger. Significantly, in native Env the tips of the fingers were directed against each other enclosing a cavity below, whereas they had turned outward in isomerization-arrested Env transforming the cavity into an open well. This might subsequently guide the fusion peptides in extended TM subunits into the target membrane.

1 - 7 of 7
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