Serviceeinheit Proteomik

Publikationen

Translation initiation of leaderless and polycistronic transcripts in mammalian mitochondria

  • Remes, C.
  • Khawaja, A.
  • Pearce, S. F.
  • Dinan, A. M.
  • Gopalakrishna, S.
  • Cipullo, M.
  • Kyriakidis, V.
  • Zhang, J.
  • Dopico, X. C.
  • Yukhnovets, O.
  • Atanassov, I.
  • Firth, A. E.
  • Cooperman, B.
  • Rorbach, J.
(2023) Nucleic Acids Res

Human mitochondria require mtRF1 for translation termination at non-canonical stop codons

  • Kruger, A.
  • Remes, C.
  • Shiriaev, D. I.
  • Liu, Y.
  • Spahr, H.
  • Wibom, R.
  • Atanassov, I.
  • Nguyen, M. D.
  • Cooperman, B. S.
  • Rorbach, J.
(2023) Nat Commun, 14, 1, 30

Mitochondria shed their outer membrane in response to infection-induced stress

  • Li, X.
  • Straub, J.
  • Medeiros, T. C.
  • Mehra, C.
  • den Brave, F.
  • Peker, E.
  • Atanassov, I.
  • Stillger, K.
  • Michaelis, J. B.
  • Burbridge, E.
  • Adrain, C.
  • Munch, C.
  • Riemer, J.
  • Becker, T.
  • Pernas, L. F.
(2022) Science, 375, 6577, eabi4343

Mechanism of mitoribosomal small subunit biogenesis and preinitiation

  • Itoh, Y.
  • Khawaja, A.
  • Laptev, I.
  • Cipullo, M.
  • Atanassov, I.
  • Sergiev, P.
  • Rorbach, J.
  • Amunts, A.
(2022) Nature, 606, 7914, 603-608

Tissue-specific modulation of gene expression in response to lowered insulin signalling in Drosophila

  • Tain, L. S.
  • Sehlke, R.
  • Meilenbrock, R. L.
  • Leech, T.
  • Paulitz, J.
  • Chokkalingam, M.
  • Nagaraj, N.
  • Gronke, S.
  • Frohlich, J.
  • Atanassov, I.
  • Mann, M.
  • Beyer, A.
  • Partridge, L.
(2021) Elife, 10

The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters

  • Schober, F. A.
  • Moore, D.
  • Atanassov, I.
  • Moedas, M. F.
  • Clemente, P.
  • Vegvari, A.
  • Fissi, N. E.
  • Filograna, R.
  • Bucher, A. L.
  • Hinze, Y.
  • The, M.
  • Hedman, E.
  • Chernogubova, E.
  • Begzati, A.
  • Wibom, R.
  • Jain, M.
  • Nilsson, R.
  • Kall, L.
  • Wedell, A.
  • Freyer, C.
  • Wredenberg, A.
(2021) Sci Adv, 7, 8

Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits

  • Schober, F. A.
  • Atanassov, I.
  • Moore, D.
  • Calvo-Garrido, J.
  • Moedas, M. F.
  • Wedell, A.
  • Freyer, C.
  • Wredenberg, A.
(2021) Mol Cell Proteomics, 20, 100065

Quantitative Proteomics in Drosophila with Holidic Stable-Isotope Labeling of Amino Acids in Fruit Flies (SILAF)

  • Schober, F. A.
  • Atanassov, I.
  • Freyer, C.
  • Wredenberg, A.
(2021) Methods Mol Biol, 2192: 75-87

Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1

  • Ruegenberg, S.
  • Mayr, Famc
  • Atanassov, I.
  • Baumann, U.
  • Denzel, M. S.
(2021) Nat Commun, 12, 1, 2176

Step-by-Step Sample Preparation of Proteins for Mass Spectrometric Analysis

  • Li, X.
  • Franz, T.
  • Atanassov, I.
  • Colby, T.
(2021) Methods Mol Biol, 2261, 13-23

Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility

  • Koester, J.
  • Miroshnikova, Y. A.
  • Ghatak, S.
  • Chacon-Martinez, C. A.
  • Morgner, J.
  • Li, X.
  • Atanassov, I.
  • Altmuller, J.
  • Birk, D. E.
  • Koch, M.
  • Bloch, W.
  • Bartusel, M.
  • Niessen, C. M.
  • Rada-Iglesias, A.
  • Wickstrom, S. A.
(2021) Nat Cell Biol, 23, 7, 771-781

The mitochondrial single-stranded DNA binding protein is essential for initiation of mtDNA replication

  • Jiang, M.
  • Xie, X.
  • Zhu, X.
  • Jiang, S.
  • Milenkovic, D.
  • Misic, J.
  • Shi, Y.
  • Tandukar, N.
  • Li, X.
  • Atanassov, I.
  • Jenninger, L.
  • Hoberg, E.
  • Albarran-Gutierrez, S.
  • Szilagyi, Z.
  • Macao, B.
  • Siira, S. J.
  • Carelli, V.
  • Griffith, J. D.
  • Gustafsson, C. M.
  • Nicholls, T. J.
  • Filipovska, A.
  • Larsson, N. G.
  • Falkenberg, M.
(2021) Sci Adv, 7, 27, eabf8631

Human GTPBP5 is involved in the late stage of mitoribosome large subunit assembly

  • Cipullo, M.
  • Pearce, S. F.
  • Lopez Sanchez, I. G.
  • Gopalakrishna, S.
  • Kruger, A.
  • Schober, F.
  • Busch, J. D.
  • Li, X.
  • Wredenberg, A.
  • Atanassov, I.
  • Rorbach, J.**
(2021) Nucleic Acids Res, 49, 1, 354-370

NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin

  • Tharyan, R. G.
  • Annibal, A.
  • Schiffer, I.
  • Laboy, R.
  • Atanassov, I.
  • Weber, A. L.
  • Gerisch, B.
  • Antebi, A.
(2020) Nat Metab, 2, 5, 387-396

Small-molecule inhibitors of human mitochondrial DNA transcription

  • Bonekamp, N. A.
  • Peter, B.
  • Hillen, H. S.
  • Felser, A.
  • Bergbrede, T.
  • Choidas, A.
  • Horn, M.
  • Unger, A.
  • Di Lucrezia, R.
  • Atanassov, I.
  • Li, X.
  • Koch, U.
  • Menninger, S.
  • Boros, J.
  • Habenberger, P.
  • Giavalisco, P.
  • Cramer, P.
  • Denzel, M. S.
  • Nussbaumer, P.
  • Klebl, B.
  • Falkenberg, M.
  • Gustafsson, C. M.
  • Larsson, N. G.
(2020) Nature, 588, 7839, 712-716

FBXL4 deficiency increases mitochondrial removal by autophagy

  • Alsina, D.
  • Lytovchenko, O.
  • Schab, A.
  • Atanassov, I.
  • Schober, F. A.
  • Jiang, M.
  • Koolmeister, C.
  • Wedell, A.
  • Taylor, R. W.
  • Wredenberg, A.
  • Larsson, N. G.
(2020) EMBO Mol Med, 12, 7, e11659

Site-specific cleavage of bacterial MucD by secreted proteases mediates antibacterial resistance in Arabidopsis

  • Wang, Y.
  • Garrido-Oter, R.
  • Wu, J.
  • Winkelmüller, T. M.
  • Agler, M.
  • Colby, T.
  • Nobori, T.
  • Kemen, E.
  • Tsuda, K.
(2019) Nat Commun, 10(1): 2853

Deregulated Splicing Is a Major Mechanism of RNA-Induced Toxicity in Huntington's Disease

  • Schilling, J.
  • Broemer, M.
  • Atanassov, I.
  • Duernberger, Y.
  • Vorberg, I.
  • Dieterich, C.
  • Dagane, A.
  • Dittmar, G.
  • Wanker, E.
  • van Roon-Mom, W.
  • Winter, J.
  • Krauss, S.
(2019) J Mol Biol, 431, 9, 1869-1877

TEFM regulates both transcription elongation and RNA processing in mitochondria

  • Jiang, S.
  • Koolmeister, C.
  • Misic, J.
  • Siira, S.
  • Kuhl, I.
  • Silva Ramos, E.
  • Miranda, M.
  • Jiang, M.
  • Posse, V.
  • Lytovchenko, O.
  • Atanassov, I.
  • Schober, F. A.
  • Wibom, R.
  • Hultenby, K.
  • Milenkovic, D.
  • Gustafsson, C. M.
  • Filipovska, A.
  • Larsson, N. G.
(2019) EMBO Rep, 20, 6

The RNA-Protein Interactome of Differentiated Kidney Tubular Epithelial Cells

  • Ignarski, M.
  • Rill, C.
  • Kaiser, R. W. J.
  • Kaldirim, M.
  • Neuhaus, R.
  • Esmaillie, R.
  • Li, X.
  • Klein, C.
  • Bohl, K.
  • Petersen, M.
  • Frese, C. K.
  • Hohne, M.
  • Atanassov, I.
  • Rinschen, M. M.
  • Hopker, K.
  • Schermer, B.
  • Benzing, T.
  • Dieterich, C.
  • Fabretti, F.
  • Muller, R. U.
(2019) J Am Soc Nephrol, 30, 4, 564-576

C6orf203 is an RNA-binding protein involved in mitochondrial protein synthesis

  • Gopalakrishna, S.
  • Pearce, S. F.
  • Dinan, A. M.
  • Schober, F. A.
  • Cipullo, M.
  • Spahr, H.
  • Khawaja, A.
  • Maffezzini, C.
  • Freyer, C.
  • Wredenberg, A.
  • Atanassov, I.
  • Firth, A. E.
  • Rorbach, J.
(2019) Nucleic Acids Res, 47, 17, 9386-9399

MitoRibo-Tag Mice Provide a Tool for In Vivo Studies of Mitoribosome Composition

  • Busch, J. D.
  • Cipullo, M.
  • Atanassov, I.
  • Bratic, A.
  • Silva Ramos, E.
  • Schondorf, T.
  • Li, X.
  • Pearce, S. F.
  • Milenkovic, D.
  • Rorbach, J.
  • Larsson, N. G.
(2019) Cell Rep, 29, 6, 1728-1738 e9

An apoplastic peptide activates salicylic acid signalling in maize

  • Ziemann, S.
  • van der Linde, K.
  • Lahrmann, U.
  • Acar, B.
  • Kaschani, F.
  • Colby, T.
  • Kaiser, M.
  • Ding, Y.
  • Schmelz, E.
  • Huffaker, A.
  • Holton, N.
  • Zipfel, C.
  • Doehlemann, G.
(2018) Nat Plants, 4(3): 172-180

Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria

  • Matic, S.
  • Jiang, M.
  • Nicholls, T. J.
  • Uhler, J. P.
  • Dirksen-Schwanenland, C.
  • Polosa, P. L.
  • Simard, M. L.
  • Li, X.
  • Atanassov, I.
  • Rackham, O.
  • Filipovska, A.
  • Stewart, J. B.
  • Falkenberg, M.
  • Larsson, N. G.
  • Milenkovic, D.
(2018) Nat Commun, 9, 1, 1202

Matching Dietary Amino Acid Balance to the In Silico-Translated Exome Optimizes Growth and Reproduction without Cost to Lifespan

  • Piper, M. D.
  • Soultoukis, G. A.
  • Blanc, E.
  • Mesaros, A.
  • Herbert, S. L.
  • Juricic, P.
  • He, X.
  • Atanassov, I.
  • Salmonowicz, H.
  • Yang, M.
  • Simpson, S. J.
  • Ribeiro, C.
  • Partridge, L.
(2017) Cell Metab, 25, 3, 610-621

Bayesian prediction of RNA translation from ribosome profiling

  • Malone, B.
  • Atanassov, I.
  • Aeschimann, F.
  • Li, X.
  • Grosshans, H.
  • Dieterich, C.
(2017) Nucleic Acids Res, 45, 6, 2960-2972

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals

  • Kuhl, I.
  • Miranda, M.
  • Atanassov, I.
  • Kuznetsova, I.
  • Hinze, Y.
  • Mourier, A.
  • Filipovska, A.
  • Larsson, N. G.
(2017) Elife, 6

Increased Total mtDNA Copy Number Cures Male Infertility Despite Unaltered mtDNA Mutation Load

  • Jiang, M.
  • Kauppila, T. E. S.
  • Motori, E.
  • Li, X.
  • Atanassov, I.
  • Folz-Donahue, K.
  • Bonekamp, N. A.
  • Albarran-Gutierrez, S.
  • Stewart, J. B.
  • Larsson, N. G.
(2017) Cell Metab, 26, 2, 429-436 e4

Serine ADP-Ribosylation Depends on HPF1

  • Bonfiglio, J. J.
  • Fontana, P.
  • Zhang, Q.
  • Colby, T.
  • Gibbs-Seymour, I.
  • Atanassov, I.
  • Bartlett, E.
  • Zaja, R.
  • Ahel, I.
  • Matic, I.
(2017) Molecular Cell, 65, 5, 932-940.e6

SLIRP stabilizes LRPPRC via an RRM-PPR protein interface

  • Spahr, H.
  • Rozanska, A.
  • Li, X.
  • Atanassov, I.
  • Lightowlers, R. N.
  • Chrzanowska-Lightowlers, Z. M.
  • Rackham, O.
  • Larsson, N. G.
(2016) Nucleic Acids Res, 44, 14, 6868-82

Hierarchical RNA Processing Is Required for Mitochondrial Ribosome Assembly

  • Rackham, O.
  • Busch, J. D.
  • Matic, S.
  • Siira, S. J.
  • Kuznetsova, I.
  • Atanassov, I.
  • Ermer, J. A
  • Shearwood, A.-M. J.
  • Richman, T. R.
  • Stewart, J. B.
  • Mourier, A.
  • Milenkovic, D.
  • Larsson, N.-G.
  • Filipovska, A.
(2016) Cell Reports, 16, 7, 1874-1890

Serine is a new target residue for endogenous ADP-ribosylation on histones

  • Leidecker, O.
  • Bonfiglio, J. J.
  • Colby, T.
  • Zhang, Q.
  • Atanassov, I.
  • Zaja, R.
  • Palazzo, L.
  • Stockum, A.
  • Ahel, I.
  • Matic, I.
(2016) Nat Chem Biol, 12, 12, 998-1000

Respiratory proteomics: from descriptive studies to personalized medicine

  • Teran, L. M.
  • Montes-Vizuet, R.
  • Li, X.
  • Franz, T.
(2015) J Proteome Res, 14, 1, 38-50

Mitofusin 2 is required to maintain mitochondrial coenzyme Q levels

  • Mourier, A.
  • Motori, E.
  • Brandt, T.
  • Lagouge, M.
  • Atanassov, I.
  • Galinier, A.
  • Rappl, G.
  • Brodesser, S.
  • Hultenby, K.
  • Dieterich, C.
  • Larsson, N. G.
(2015) Journal of Cell Biology, 208, 4, 429-442

Step-by-step preparation of proteins for mass spectrometric analysis

  • Franz, T.
  • Li, X.
(2015) Methods Mol Biol, 1295, 235-47

Up to date sample preparation of proteins for mass spectrometric analysis

  • Li, X.
  • Franz, T.
(2014) Arch Physiol Biochem, 120, 5, 188-91

Secretome profiling of primary human skeletal muscle cells

  • Hartwig, S.
  • Raschke, S.
  • Knebel, B.
  • Scheler, M.
  • Irmler, M.
  • Passlack, W.
  • Muller, S.
  • Hanisch, F. G.
  • Franz, T.
  • Li, X.
  • Dicken, H. D.
  • Eckardt, K.
  • Beckers, J.
  • de Angelis, M. H.
  • Weigert, C.
  • Haring, H. U.
  • Al-Hasani, H.
  • Ouwens, D. M.
  • Eckel, J.
  • Kotzka, J.
  • Lehr, S.
(2014) Biochim Biophys Acta, 1844, 5, 1011-7

Transient antiangiogenic treatment improves delivery of cytotoxic compounds and therapeutic outcome in lung cancer

  • Chatterjee, S.
  • Wieczorek, C.
  • Schottle, J.
  • Siobal, M.
  • Hinze, Y.
  • Franz, T.
  • Florin, A.
  • Adamczak, J.
  • Heukamp, L. C.
  • Neumaier, B.
  • Ullrich, R. T.
(2014) Cancer Res, 74, 10, 2816-24

2D-ToGo workflow: increasing feasibility and reproducibility of 2-dimensional gel electrophoresis

  • Posch, A.
  • Franz, T.
  • Hartwig, S.
  • Knebel, B.
  • Al-Hasani, H.
  • Passlack, W.
  • Kunz, N.
  • Hinze, Y.
  • Li, X.
  • Kotzka, J.
  • Lehr, S.
(2013) Arch Physiol Biochem, 119, 3, 108-13

The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry

  • Hess, M. E.
  • Hess, S.
  • Meyer, K. D.
  • Verhagen, L. A.
  • Koch, L.
  • Bronneke, H. S.
  • Dietrich, M. O.
  • Jordan, S. D.
  • Saletore, Y.
  • Elemento, O.
  • Belgardt, B. F.
  • Franz, T.
  • Horvath, T. L.
  • Ruther, U.
  • Jaffrey, S. R.
  • Kloppenburg, P.
  • Bruning, J. C.
(2013) Nat Neurosci, 16, 8, 1042-8

Monomeric nucleoprotein of influenza A virus

  • Chenavas, S.
  • Estrozi, L. F.
  • Slama-Schwok, A.
  • Delmas, B.
  • Di Primo, C.
  • Baudin, F.
  • Li, X.
  • Crepin, T.
  • Ruigrok, R. W.
(2013) PLoS Pathog, 9, 3, e1003275

Immune Response to Seasonal Influenza A Virus Infection: A Proteomic Approach

  • Teran, L. M.
  • Ruggeberg, S.
  • Santiago, J.
  • Fuentes-Arenas, F.
  • Hernandez, J. L.
  • Montes-Vizuet, A. R.
  • Li, X. P.
  • Franz, T.
(2012) Archives of Medical Research, 43, 6, 464-469

The OASIS (R) HLB mu Elution plate as a one-step platform for manual high-throughput in-gel digestion of proteins and peptide desalting

  • Franz, T.
  • Li, X. P.
(2012) Proteomics, 12, 15-16, 2487-2492

MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome

  • Camara, Y.
  • Asin-Cayuela, J.
  • Park, C. B.
  • Metodiev, M. D.
  • Shi, Y.
  • Ruzzenente, B.
  • Kukat, C.
  • Habermann, B.
  • Wibom, R.
  • Hultenby, K.
  • Franz, T.
  • Erdjument-Bromage, H.
  • Tempst, P.
  • Hallberg, B. M.
  • Gustafsson, C. M.
  • Larsson, N. G.
(2011) Cell Metab, 13, 5, 527-39

Molecular variability of FLT3/ITD mutants and their impact on the differentiation program of 32D cells: Implications for the biological properties of AML blasts

  • Pekova, S.
  • Ivanek, R.
  • Dvorak, M.
  • Rueggeberg, S.
  • Leicht, S.
  • Li, X. P.
  • Franz, T.
  • Kozak, T.
  • Vrba, J.
  • Koza, V.
  • Karas, M.
  • Schwarz, J.
  • Cetkovsky, P.
  • Prucha, M.
(2009) Leukemia Research, 33, 10, 1409-1416