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  • 1.
    Asayesh, Amir
    et al.
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Sharpe, James
    Watson, Robert P
    Hecksher-Sørensen, Jacob
    Hastie, Nicholas D
    Hill, Robert E
    Ahlgren, Ulf
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Spleen versus pancreas: strict control of organ interrelationship revealed by analyses of Bapx1-/- mice.2006In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 20, no 16, p. 2208-2213Article in journal (Refereed)
  • 2. Garg, Parie
    et al.
    Stith, Carrie M
    Sabouri, Nasim
    Umeå University, Faculty of Medicine, Medical Biochemistry and Biophsyics.
    Johansson, Erik
    Umeå University, Faculty of Medicine, Medical Biochemistry and Biophsyics.
    Burgers, Peter M
    Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication.2004In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 18, no 22, p. 2764-2773Article in journal (Refereed)
  • 3. Jishage, Miki
    et al.
    Kvint, Kristian
    Shingler, Victoria
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Nyström, Thomas
    Regulation of sigma factor competition by the alarmone ppGpp2002In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 16, no 10, p. 1260-1270Article in journal (Refereed)
    Abstract [en]

    Many regulons controlled by alternative ç factors, including çs and ç32, are poorly induced in cells lacking the alarmone ppGpp. We show that ppGpp is not absolutely required for the activity of çs-dependent promoters because underproduction of ç70, specific mutations in rpoD (rpoD40 and rpoD35), or overproduction of Rsd (anti-ç70) restored expression from çs-dependent promoters in vivo in the absence of ppGpp accumulation. An in vitro transcription/competition assay with reconstituted RNA polymerase showed that addition of ppGpp reduces the ability of wild-type ç70 to compete with ç32 for core binding and the mutant ç70 proteins, encoded by rpoD40 and rpoD35, compete less efficiently than wild-type ç70. Similarly, an in vivo competition assay showed that the ability of both sigma(32) and sigma(S) to compete with sigma(70) is diminished in cells lacking ppGpp. Consistently, the fraction of çs and ç32 bound to core was drastically reduced in ppGpp-deficient cells. Thus, the stringent response encompasses a mechanism that alters the relative competitiveness of sigma factors in accordance with cellular demands during physiological stress.

  • 4.
    Johansson, Marcus JO
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Jacobson, Allan
    University Massachusetts, School of Medicine, Dept Mol Genet & Microbiol, Worcester, MA .
    Nonsense-mediated mRNA decay maintains translational fidelity by limiting magnesium uptake2010In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 24, no 14, p. 1491-1495Article in journal (Refereed)
    Abstract [en]

    Inactivation of the yeast nonsense-mediated mRNA decay (NMD) pathway stabilizes nonsense mRNAs and promotes readthrough of premature translation termination codons. Although the latter phenotype is thought to reflect a direct role of NMD factors in translation termination, its mechanism is unknown. Here we show that the reduced termination efficiency of NMD-deficient cells is attributable to increased expression of the magnesium transporter Alr1p and the resulting effects of elevated Mg2+ levels on termination fidelity. Alr1p levels increase because an upstream ORF in ALR1 mRNA targets the transcript for NMD. Our results demonstrate that NMD, at least in yeast, controls Mg2+ homeostasis and, consequently, translational fidelity.

  • 5. Lanz, Michael Charles
    et al.
    Oberly, Susannah
    Sanford, Ethan James
    Sharma, Sushma
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Chabes, Andrei
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Smolka, Marcus Bustamante
    Separable roles for Mec1/ATR in genome maintenance, DNA replication, and checkpoint signaling2018In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 32, no 11-12, p. 822-835Article in journal (Refereed)
    Abstract [en]

    The Mec1/ATR kinase coordinates multiple cellular responses to replication stress. In addition to its canonical role in activating the checkpoint kinase Rad53, Mec1 also plays checkpoint-independent roles in genome maintenance that are not well understood. Here we used a combined genetic-phosphoproteomic approach to manipulate Mec1 activation and globally monitor Mec1 signaling, allowing us to delineate distinct checkpoint-independent modes of Mec1 action. Using cells in which endogenous Mec1 activators were genetically ablated, we found that expression of "free" Mec1 activation domains (MADs) can robustly activate Mec1 and rescue the severe DNA replication and growth defects of these cells back to wild-type levels. However, unlike the activation mediated by endogenous activator proteins, "free" MADs are unable to stimulate Mec1-mediated suppression of gross chromosomal rearrangements (GCRs), revealing that Mec1's role in genome maintenance is separable from a previously unappreciated proreplicative function. Both Mec1's functions in promoting replication and suppressing GCRs are independent of the downstream checkpoint kinases. Additionally, Mec1-dependent GCR suppression seems to require localized Mec1 action at DNA lesions, which correlates with the phosphorylation of activator-proximal substrates involved in homologous recombination-mediated DNA repair. These findings establish that Mec1 initiates checkpoint signaling, promotes DNA replication, and maintains genetic stability through distinct modes of action.

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  • 6. Liu, Yanjie
    et al.
    Tewari, Rita
    Ning, Jue
    Blagborough, Andrew M
    Garbom, Sara
    Pei, Jimin
    Grishin, Nick V
    Steele, Robert E
    Sinden, Robert E
    Snell, William J
    Billker, Oliver
    Division of Cell and Molecular Biology, Imperial College London; The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom London, United Kingdom; .
    The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes2008In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 22, no 8, p. 1051-1068Article in journal (Refereed)
    Abstract [en]

    The cellular and molecular mechanisms that underlie species-specific membrane fusion between male and female gametes remain largely unknown. Here, by use of gene discovery methods in the green alga Chlamydomonas, gene disruption in the rodent malaria parasite Plasmodium berghei, and distinctive features of fertilization in both organisms, we report discovery of a mechanism that accounts for a conserved protein required for gamete fusion. A screen for fusion mutants in Chlamydomonas identified a homolog of HAP2, an Arabidopsis sterility gene. Moreover, HAP2 disruption in Plasmodium blocked fertilization and thereby mosquito transmission of malaria. HAP2 localizes at the fusion site of Chlamydomonas minus gametes, yet Chlamydomonas minus and Plasmodium hap2 male gametes retain the ability, using other, species-limited proteins, to form tight prefusion membrane attachments with their respective gamete partners. Membrane dye experiments show that HAP2 is essential for membrane merger. Thus, in two distantly related eukaryotes, species-limited proteins govern access to a conserved protein essential for membrane fusion.

  • 7. Lundström, Annika
    et al.
    Gallio, Marco
    Englund, Camilla
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Pathogenesis (UCMP) (Faculty of Medicine).
    Steneberg, Pär
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Pathogenesis (UCMP) (Faculty of Medicine).
    Hemphälä, Johanna
    Aspenström, Pontus
    Keleman, Krystyna
    Falileeva, Ludmilla
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Pathogenesis (UCMP) (Faculty of Medicine).
    Dickson, Barry J
    Samakovlis, Christos
    Vilse, a conserved Rac/Cdc42 GAP mediating Robo repulsion in tracheal cells and axons2004In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 18, no 17, p. 2161-71Article in journal (Refereed)
    Abstract [en]

    Slit proteins steer the migration of many cell types through their binding to Robo receptors, but how Robo controls cell motility is not clear. We describe the functional analysis of vilse, a Drosophila gene required for Robo repulsion in epithelial cells and axons. Vilse defines a conserved family of RhoGAPs (Rho GTPase-activating proteins), with representatives in flies and vertebrates. The phenotypes of vilse mutants resemble the tracheal and axonal phenotypes of Slit and Robo mutants at the CNS midline. Dosage-sensitive genetic interactions between vilse, slit, and robo mutants suggest that vilse is a component of robo signaling. Moreover, overexpression of Vilse in the trachea of robo mutants ameliorates the phenotypes of robo, indicating that Vilse acts downstream of Robo to mediate midline repulsion. Vilse and its human homolog bind directly to the intracellular domains of the corresponding Robo receptors and promote the hydrolysis of RacGTP and, less efficiently, of Cdc42GTP. These results together with genetic interaction experiments with robo, vilse, and rac mutants suggest a mechanism whereby Robo repulsion is mediated by the localized inactivation of Rac through Vilse.

  • 8. Ning, Jue
    et al.
    Otto, Thomas D.
    Pfander, Claudia
    Schwach, Frank
    Brochet, Mathieu
    Bushell, Ellen
    Goulding, David
    Sanders, Mandy
    Lefebvre, Paul A.
    Pei, Jimin
    Grishin, Nick V.
    Vanderlaan, Gary
    Billker, Oliver
    Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, United Kingdom.
    Snell, William J.
    Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates2013In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 27, no 10, p. 1198-1215Article in journal (Refereed)
    Abstract [en]

    Fertilization is a crucial yet poorly characterized event in eukaryotes. Our previous discovery that the broadly conserved protein HAP2 (GCS1) functioned in gamete membrane fusion in the unicellular green alga Chlamydomonas and the malaria pathogen Plasmodium led us to exploit the rare biological phenomenon of isogamy in Chlamydomonas in a comparative transcriptomics strategy to uncover additional conserved sexual reproduction genes. All previously identified Chlamydomonas fertilization-essential genes fell into related clusters based on their expression patterns. Out of several conserved genes in a minus gamete cluster, we focused on Cre06.g280600, an ortholog of the fertilization-related Arabidopsis GEX1. Gene disruption, cell biological, and immunolocalization studies show that CrGEX1 functions in nuclear fusion in Chlamydomonas. Moreover, CrGEX1 and its Plasmodium ortholog, PBANKA_113980, are essential for production of viable meiotic progeny in both organisms and thus for mosquito transmission of malaria. Remarkably, we discovered that the genes are members of a large, previously unrecognized family whose first-characterized member, KAR5, is essential for nuclear fusion during yeast sexual reproduction. Our comparative transcriptomics approach provides a new resource for studying sexual development and demonstrates that exploiting the data can lead to the discovery of novel biology that is conserved across distant taxa.

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  • 9.
    Park, Hyun-Sook
    et al.
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Östberg, Yngve
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Johansson, Jörgen
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Wagner, E Gerhart
    Uhlin, Bernt Eric
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Novel role for a bacterial nucleoid protein in translation of mRNAs with suboptimal ribosome-binding sites2010In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 24, no 13, p. 1345-1350Article in journal (Refereed)
    Abstract [en]

    In Escherichia coli, the major nucleoid protein H-NS limits transcription by acting as a repressor or transcriptional silencer, presumably by its ability to close the looped chromosome domains in the nucleoid through DNA-protein-DNA bridging. Here, we demonstrate the direct involvement of H-NS as a positive factor stimulating translation of the malT mRNA. In vitro studies showed that H-NS facilitates a repositioning of the 30S preinitiation complex on the malT mRNA. H-NS stimulation of translation depended on the AU-rich -35 to -40 region of the mRNA. Several additional examples were found demonstrating a novel function for H-NS in translation of genes with suboptimal ribosome-binding sequences.

  • 10.
    Sabouri, Nasim
    et al.
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
    McDonald, Karin R
    Webb, Christopher J
    Cristea, Ileana M
    Zakian, Virginia A
    DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase2012In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 26, no 6, p. 581-593Article in journal (Refereed)
    Abstract [en]

    Replication forks encounter impediments as they move through the genome, including natural barriers due to stable protein complexes and highly transcribed genes. Unlike lesions generated by exogenous damage, natural barriers are encountered in every S phase. Like humans, Schizosaccharomyces pombe encodes a single Pif1 family DNA helicase, Pfh1. Here, we show that Pfh1 is required for efficient fork movement in the ribosomal DNA, the mating type locus, tRNA, 5S ribosomal RNA genes, and genes that are highly transcribed by RNA polymerase II. In addition, converged replication forks accumulated at all of these sites in the absence of Pfh1. The effects of Pfh1 on DNA replication are likely direct, as it had high binding to sites whose replication was impaired in its absence. Replication in the absence of Pfh1 resulted in DNA damage specifically at those sites that bound high levels of Pfh1 in wild-type cells and whose replication was slowed in its absence. Cells depleted of Pfh1 were inviable if they also lacked the human TIMELESS homolog Swi1, a replisome component that stabilizes stalled forks. Thus, Pfh1 promotes DNA replication and separation of converged replication forks and suppresses DNA damage at hard-to-replicate sites.

  • 11. Schrick, K.
    et al.
    Mayer, U.
    Horrichs, A.
    Kuhnt, C.
    Bellini, C.
    Dangl, J.
    Schmidt, J.
    Jurgens, G.
    FACKEL is a sterol C-14 reductase required for organized cell division and expansion in Arabidopsis embryogenesis2000In: Genes & Development, ISSN 0890-9369, E-ISSN 1549-5477, Vol. 14, no 12, p. 1471-1484, article id 10859166Article in journal (Refereed)
    Abstract [en]

    In flowering plants, the developing embryo consists of growing populations of cells whose fates are determined in a position-dependent manner to form the adult organism. Mutations in the FACKEL (FK) gene affect body organization of the Arabidopsis seedling. We report that FK is required for cell division and expansion and is involved in proper organization of the embryo. We isolated FK by positional cloning. Expression analysis in embryos revealed that FK mRNA becomes localized to meristematic zones. FK encodes a predicted integral membrane protein related to the vertebrate lamin B receptor and sterol reductases across species, including yeast sterol C-14 reductase ERG24. We provide functional evidence that FK encodes a sterol C-14 reductase by complementation of erg24. GC/MS analysis confirmed that fk mutations lead to accumulation of intermediates in the biosynthetic pathway preceding the C-14 reductase step. Although fk represents a sterol biosynthetic mutant, the phenotype was not rescued by feeding with brassinosteroids (BRs), the only plant sterol signaling molecules known so far. We propose that synthesis of sterol signals in addition to BRs is important in mediating regulated cell growth and organization during embryonic development. Our results indicate a novel role for sterols in the embryogenesis of plants.

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