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  • 1. Beck, Halfdan
    et al.
    Nahse, Viola
    Larsen, Marie Sofie Yoo
    Groth, Petra
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Clancy, Trevor
    Lees, Michael
    Jörgensen, Mette
    Helleday, Thomas
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Syljuasen, Randi G.
    Sörensen, Claus Storgaard
    Regulators of cyclin-dependent kinases are crucial for maintaining genome integrity in S phase2010In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 188, no 5, p. 629-638Article in journal (Refereed)
    Abstract [en]

    Maintenance of genome integrity is of critical importance to cells. To identify key regulators of genomic integrity, we screened a human cell line with a kinome small interfering RNA library. WEE1, a major regulator of mitotic entry, and CHK1 were among the genes identified. Both kinases are important negative regulators of CDK1 and -2. Strikingly, WEE1 depletion rapidly induced DNA damage in S phase in newly replicated DNA, which was accompanied by a marked increase in single-stranded DNA. This DNA damage is dependent on CDK1 and -2 as well as the replication proteins MCM2 and CDT1 but not CDC25A. Conversely, DNA damage after CHK1 inhibition is highly dependent on CDC25A. Furthermore, the inferior proliferation of CHK1-depleted cells is improved substantially by codepletion of CDC25A. We conclude that the mitotic kinase WEE1 and CHK1 jointly maintain balanced cellular control of Cdk activity during normal DNA replication, which is crucial to prevent the generation of harmful DNA lesions during replication.

  • 2.
    Björk, Petra
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biology and Functional Genomics.
    Jin, ShaoBo
    Zhao, Jian
    Singh, Om Prakash
    Persson, Jan-Olov
    Stockholm University, Faculty of Science, Department of Mathematics.
    Hellman, Ulf
    Wieslander, Lars
    Stockholm University, Faculty of Science, Department of Molecular Biology and Functional Genomics.
    Specific combinations of SR proteins associate with single pre-messenger RNAs in vivo and contribute different functions2009In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 184, no 4, p. 555-568Article in journal (Refereed)
    Abstract [en]

    Serine/arginine-rich (SR) proteins are required for messenger RNA (mRNA) processing, export, surveillance, and translation. We show that in Chironomus tentans, nascent transcripts associate with multiple types of SR proteins in specific combinations. Alternative splicing factor (ASF)/SF2, SC35, 9G8, and hrp45/SRp55 are all present in Balbiani ring (BR) pre-messenger ribonucleoproteins (mRNPs) preferentially when introns appear in the pre-mRNA and when cotranscriptional splicing takes place. However, hrp45/SRp55 is distributed differently in the pre-mRNPs along the gene compared with ASF/SF2, SC35, and 9G8, suggesting functional differences. All four SR proteins are associated with the BR mRNPs during export to the cytoplasm. Interference with SC35 indicates that SC35 is important for the coordination of splicing, transcription, and 3′ end processing and also for nucleocytoplasmic export. ASF/SF2 is associated with polyribosomes, whereas SC35, 9G8, and hrp45/SRp55 cosediment with monoribosomes. Thus, individual endogenous pre-mRNPs/mRNPs bind multiple types of SR proteins during transcription, and these SR proteins accompany the mRNA and play different roles during the gene expression pathway in vivo.

  • 3.
    Björk, Petra
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Persson, Jan-Olov
    Stockholm University, Faculty of Science, Department of Mathematics.
    Wieslander, Lars
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo2015In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 211, no 1, p. 63-75Article in journal (Refereed)
    Abstract [en]

    Eukaryotic gene expression requires the ordered association of numerous factors with precursor messenger RNAs (premRNAs)/messenger RNAs (mRNAs) to achieve efficiency and regulation. Here, we use the Balbiani ring (BR) genes to demonstrate the temporal and spatial association of the exon junction complex (EJC) core with gene-specific endogenous premRNAs and mRNAs. The EJC core components bind cotranscriptionally to BR premRNAs during or very rapidly after splicing. The EJC core does not recruit the nonsense-mediated decay mediaters UPF2 and UPF3 until the BR messenger RNA protein complexes (mRNPs) enter the interchromatin. Even though several known adapters for the export factor NXF1 become part of BR mRNPs already at the gene, NXF1 binds to BR mRNPs only in the interchromatin. In steady state, a subset of the BR mRNPs in the interchromatin binds NXF1, UPF2, and UPF3. This binding appears to occur stochastically, and the efficiency approximately equals synthesis and export of the BR mRNPs. Our data provide unique in vivo information on how export competent eukaryotic mRNPs are formed.

  • 4.
    Gruschke, Steffi
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kehrein, Kirsten
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Roempler, Katharina
    Groene, Kerstin
    Israel, Lars
    Imhof, Axel
    Herrmann, Johannes M.
    Ott, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Cbp3-Cbp6 interacts with the yeast mitochondrial ribosomal tunnel exit and promotes cytochrome b synthesis and assembly2011In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 193, no 6, p. 1101-1114Article in journal (Refereed)
    Abstract [en]

    Mitochondria contain their own genetic system to express a small number of hydrophobic polypeptides, including cytochrome b, an essential subunit of the bc(1) complex of the respiratory chain. In this paper, we show in yeast that Cbp3, a bc(1) complex assembly factor, and Cbp6, a regulator of cytochrome b translation, form a complex that associates with the polypeptide tunnel exit of mitochondrial ribosomes and that exhibits two important functions in the biogenesis of cytochrome b. On the one hand, the interaction of Cbp3 and Cbp6 with mitochondrial ribosomes is necessary for efficient translation of cytochrome b messenger ribonucleic acid or transcript. On the other hand, the Cbp3-Cbp6 complex interacts directly with newly synthesized cytochrome b in an assembly intermediate that is not ribosome bound and that contains the assembly factor Cbp4. Our results suggest that synthesis of cytochrome b occurs preferentially on those ribosomes that have the Cbp3-Cbp6 complex bound to their tunnel exit, an arrangement that may ensure tight coordination of cytochrome b synthesis and assembly.

  • 5.
    Gruschke, Steffi
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Römpler, Katharina
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hildenbeutel, Markus
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kehrein, Kirsten
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kuehl, Inge
    Bonnefoy, Nathalie
    Ott, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    The Cbp3-Cbp6 complex coordinates cytochrome b synthesis with bc(1) complex assembly in yeast mitochondria2012In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 199, no 1, p. 137-150Article in journal (Refereed)
    Abstract [en]

    Respiratory chain complexes in mitochondria are assembled from subunits derived from two genetic systems. For example, the bc1 complex consists of nine nuclear encoded subunits and the mitochondrially encoded subunit cytochrome b. We recently showed that the Cbp3-Cbp6 complex has a dual function for biogenesis of cytochrome b: it is both required for efficient synthesis of cytochrome b and for protection of the newly synthesized protein from proteolysis. Here, we report that Cbp3-Cbp6 also coordinates cytochrome b synthesis with bc1 complex assembly. We show that newly synthesized cytochrome b assembled through a series of four assembly intermediates. Blocking assembly at early and intermediate steps resulted in sequestration of Cbp3-Cbp6 in a cytochrome b-containing complex, thereby making Cbp3-Cbp6 unavailable for cytochrome b synthesis and thus reducing overall cytochrome b levels. This feedback loop regulates protein synthesis at the inner mitochondrial membrane by directly monitoring the efficiency of bc1 complex assembly.

  • 6.
    Hildenbeutel, Markus
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hegg, Eric L.
    Stephan, Katharina
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gruschke, Steffi
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Meunier, Brigitte
    Ott, Martin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Assembly factors monitor sequential hemylation of cytochrome b to regulate mitochondria! translation2014In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 205, no 4, p. 511-524Article in journal (Refereed)
    Abstract [en]

    Mitochondrial respiratory chain complexes convert chemical energy into a membrane potential by connecting electron transport with charge separation. Electron transport relies on redox cofactors that occupy strategic positions in the complexes. How these redox cofactors are assembled into the complexes is not known. Cytochrome b, a central catalytic subunit of complex III, contains two henne bs. Here, we unravel the sequence of events in the mitochondrial inner membrane by which cytochrome b is hemylated. Heme incorporation occurs in a strict sequential process that involves interactions of the newly synthesized cytochrome b with assembly factors and structural complex III subunits. These interactions are functionally connected to cofactor acquisition that triggers the progression of cytochrome b through successive assembly intermediates. Failure to hemylate cytochrome b sequesters the Cbp3-Cbp6 complex in early assembly intermediates, thereby causing a reduction in cytochrome b synthesis via a feedback loop that senses hemylation of cytochrome b.

  • 7.
    Jorgensen, Stine
    et al.
    University of Copenhagen, Biotech Research and Innovation Centre.
    Elvers, Ingegerd
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Beck Trelle, Morten
    University of Southern Denmark, Centre for Epigenetics, Department of Biochemistry and Molecular Biology.
    Menzel, Tobias
    University of Copenhagen, Biotech Research and Innovation Centre.
    Eskildsen, Morten
    University of Copenhagen, Biotech Research and Innovation Centre.
    Norregaard Jensen, Ole
    University of Southern Denmark, Centre for Epigenetics, Department of Biochemistry and Molecular biology.
    Helleday, Thomas
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Helin, Kristian
    University of Copenhagen, Biotech Research and Innovation Centre.
    Storgaard Sorensen, Claus
    University of Copenhagen, Biotech Research and Innovation Centre.
    The histone methyltransferase SET8 is required for S-phase progression2007In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 179, no 7, p. 1337-1345Article in journal (Refereed)
    Abstract [en]

    Chromatin structure and function is influenced by histone posttranslational modifications. SET8 (also known as PR-Set7 and SETD8) is a histone methyltransferase that monomethylates histone H4-K20. However, a function for SET8 in mammalian cell proliferation has not been determined. We show that small interfering RNA inhibition of SET8 expression leads to decreased cell proliferation and accumulation of cells in S phase. This is accompanied by DNA double-strand break (DSB) induction and recruitment of the DNA repair proteins replication protein A, Rad51, and 53BP1 to damaged regions. SET8 depletion causes DNA damage specifically during replication, which induces a Chk1-mediated S-phase checkpoint. Furthermore, we find that SET8 interacts with proliferating cell nuclear antigen through a conserved motif, and SET8 is required for DNA replication fork progression. Finally, codepletion of Rad51, an improtant homologous recombination repair protein, abrogates the DNA damage after SET8 depletion. Overall, we show that SET8 is essential for genomic stability in mammalian cells and that decreased expression of SET8 results in DNA damage and Chk1-dependent S-phase arrest.

  • 8.
    Kiesler, Eva
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biology and Functional Genomics.
    Hase, Manuela
    Visa, Neus
    Hrp59, an hnRNP M-like protein in Chironomus and Drosophila, binds to exonic splicing enhancers in a subset of pre-mRNAs2004In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 168, no 7, p. 1031-1025Article in journal (Refereed)
    Abstract [en]

    Here, we study an insect hnRNP M protein, referred to as Hrp59. Hrp59 is relatively abundant, has a modular domain organization containing three RNA-binding domains, is dynamically recruited to transcribed genes, and binds to premRNA cotranscriptionally. Using the Balbiani ring system of Chironomus, we show that Hrp59 accompanies the mRNA from the gene to the nuclear envelope, and is released from the mRNA at the nuclear pore. The association of Hrp59 with transcribed genes is not proportional to the amount of synthesized RNA, and in vivo Hrp59 binds preferentially to a subset of mRNAs, including its own mRNA. By coimmunoprecipitation of Hrp59-RNA complexes and microarray hybridization against Drosophila whole-genome arrays, we identify the preferred mRNA targets of Hrp59 in vivo and show that Hrp59 is required for the expression of these target mRNAs. We also show that Hrp59 binds preferentially to exonic splicing enhancers and our results provide new insights into the role of hnRNP M in splicing regulation.

  • 9.
    Nilsson, IngMarie
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Texas A&M University System Health Science Center, Texas.
    Kelleher, Daniel J.
    Miao, Yiwei
    Shao, Yuanlong
    Kreibich, Gert
    Gilmore, Reid
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Johnson, Arthur E.
    Photocross-linking of nascent chains to the STT3 subunit of the oligosaccharyltransferase complex2003In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 161, no 4, p. 715-725Article in journal (Refereed)
    Abstract [en]

    In eukaryotic cells, polypeptides are N glycosylated after passing through the membrane of the ER into the ER lumen. This modification is effected cotranslationally by the multimeric oligosaccharyltransferase (OST) enzyme. Here, we report the first cross-linking of an OST subunit to a nascent chain that is undergoing translocation through, or integration into, the ER membrane. A photoreactive probe was incorporated into a nascent chain using a modified Lys-tRNA and was positioned in a cryptic glycosylation site (-Q-K-T- instead of -N-K-T-) in the nascent chain. When translocation intermediates with nascent chains of increasing length were irradiated, nascent chain photocross-linking to translocon components, Sec61alpha and TRAM, was replaced by efficient photocross-linking solely to a protein identified by immunoprecipitation as the STT3 subunit of the OST No cross-linking was observed in the absence of a cryptic sequence or in the presence of a competitive peptide substrate of the OST. As no significant nascent chain photocross-linking to other OST subunits was detected in these fully assembled translocation and integration intermediates, our results strongly indicate that the nascent chain portion of the OST active site is located in STT3.

  • 10.
    Nordholm, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Petitou, Jeanne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Östbye, Henrik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    da Silva, Diogo V.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Dou, Dan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Wang, Hao
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Daniels, Robert
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Translational regulation of viral secretory proteins by the 5 ' coding regions and a viral RNA-binding protein2017In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 216, no 8, p. 2283-2293Article in journal (Refereed)
    Abstract [en]

    A primary function of 5' regions in many secretory protein mRNAs is to encode an endoplasmic reticulum (ER) targeting sequence. In this study, we show how the regions coding for the ER-targeting sequences of the influenza glycoproteins NA and HA also function as translational regulatory elements that are controlled by the viral RNA-binding protein (RBP) NS1. The translational increase depends on the nucleotide composition and 5' positioning of the ER-targeting sequence coding regions and is facilitated by the RNA-binding domain of NS1, which can associate with ER membranes. Inserting the ER-targeting sequence coding region of NA into different 5' UTRs confirmed that NS1 can promote the translation of secretory protein mRNAs based on the nucleotides within this region rather than the resulting amino acids. By analyzing human protein mRNA sequences, we found evidence that this mechanism of using 5' coding regions and particular RBPs to achieve gene-specific regulation may extend to human-secreted proteins.

  • 11.
    Nordholm, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Petitou, Jeanne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Östbye, Henrik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Vieira da Silva, Diogo
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Dou, Dan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Wang, Hao
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Daniels, Robert
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Translational regulation of viral secretory proteins by 5’ coding regions and a viral RNA-binding proteinIn: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140Article in journal (Refereed)
    Abstract [en]

    A primary function of 5’ regions in many secretory protein mRNAs is to encode an endoplasmic reticulum (ER) targeting sequence. Here we show the regions coding for the ER-targeting sequences of the influenza proteins NA and HA also function as translational regulatory elements, which are controlled by the viral RNA-binding protein NS1. The translational increase depends on the nucleotide composition of the NA and HA ER-targeting sequences, their 5’ positioning, and is facilitated by the NS1 RNA-binding domain, which can associate with ER membranes. Inserting the ER-targeting sequence coding region of NA into different 5’UTRs confirmed that NS1 can promote the translation of secretory protein mRNAs based on the nucleotides within this region rather than the resulting amino acids. By analysing human protein mRNA sequences we found evidence that this mechanism of using 5’ coding regions and particular RNA-binding proteins to achieve gene-specific regulation may extend to human secreted proteins.

  • 12.
    Olsen, Jessica M.
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Sato, Masaaki
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Monash Institute of Pharmaceutical Sciences, Australia.
    Dallner, Olof S.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. The Rockefeller University, USA.
    Sandström, Anna L.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Pisani, Didier F.
    Jean-Claude, Chambard
    Amri, Ez-Zoubir
    Hutchinson, Dana S.
    Bengtsson, Tore
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Glucose uptake in brown fat cells is dependent on mTOR complex 2-promoted GLUT1 translocation2014In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 207, no 3, article id 365Article in journal (Refereed)
    Abstract [en]

    Brown adipose tissue is the primary site for thermogenesis and can consume, in addition to free fatty acids, a very high amount of glucose from the blood, which can both acutely and chronically affect glucose homeostasis. Here, we show that mechanistic target of rapamycin (mTOR) complex 2 has a novel role in β3-adrenoceptor-stimulated glucose uptake in brown adipose tissue. We show that β3-adrenoceptors stimulate glucose uptake in brown adipose tissue via a signaling pathway that is comprised of two different parts: one part dependent on cAMP-mediated increases in GLUT1 transcription and de novo synthesis of GLUT1 and another part dependent on mTOR complex 2-stimulated translocation of newly synthesized GLUT1 to the plasma membrane, leading to increased glucose uptake. Both parts are essential for β3-adrenoceptor-stimulated glucose uptake. Importantly, the effect of β3-adrenoceptor on mTOR complex 2 is independent of the classical insulin-phosphoinositide 3-kinase-Akt pathway, highlighting a novel mechanism of mTOR complex 2 activation.

  • 13. Skouloudaki, Kassiani
    et al.
    Christodoulou, Ioannis
    Khalili, Dilan
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Tsarouhas, Vaeos
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Samakovlis, Christos
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. University of Giessen, Germany..
    Tomancak, Pavel
    Knust, Elisabeth
    Papadopoulos, Dimitrios K.
    Yorkie controls tube length and apical barrier integrity during airway development2019In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 218, no 8, p. 2762-2781Article in journal (Refereed)
    Abstract [en]

    Epithelial organ size and shape depend on cell shape changes, cell-matrix communication, and apical membrane growth. The Drosophila melanogaster embryonic tracheal network is an excellent model to study these processes. Here, we show that the transcriptional coactivator of the Hippo pathway, Yorkie (YAP/TAZ in vertebrates), plays distinct roles in the developing Drosophila airways. Yorkie exerts a cytoplasmic function by binding Drosophila Twinstar, the orthologue of the vertebrate actin-severing protein Cofilin, to regulate F-actin levels and apical cell membrane size, which are required for proper tracheal tube elongation. Second, Yorkie controls water tightness of tracheal tubes by transcriptional regulation of the d-aminolevulinate synthase gene (Alas). We conclude that Yorkie has a dual role in tracheal development to ensure proper tracheal growth and functionality.

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