Publications

2018

JBC March 2018 Cover

Structure of S. aureus RelP, cover of the Journal of Biological Chemistry (Manav et al., 2018)

Hove-Jensen, B., Brodersen, D. E., and Manav, M. C. (2018) “The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism”, Microbiol Mol Biol Rev, 83(1): e00040-18.

Skjerning, R. B., Senissar, M., Winther, K. S., Gerdes, K., and Brodersen, D. E. (2018) “The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD+“, Mol Microbiol, 111(1): 221-236.

Manav, M. C., Sofos, N., Hove-Jensen, B., and Brodersen, D. E. (2018) “The ABC of phosphonate breakdown: A mechanism for bacterial survival”, BioEssays, 40(11): e1800091.

He, F., Bhoobalan-Chitty, Y., Van, L. B., Kjeldsen, A. L., Dedola, M., Makarova, K., Koonin, E. V., Brodersen, D. E., Peng, X. (2018) “Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity”, Nat Microbiol, 3(4):461-9 (PubMed).

Harms, A., Brodersen, D. E., Mitarai, N., Gerdes, K. (2018) “Toxins, targets, and triggers: An overview of toxin-antitoxin biology”, Mol Cell, 70(5):768-784 (PubMed).

Manav, M. C., Beljantseva, J., Bojer, M. S., Tenson, T., Ingmer, H., Hauryliuk, V., Brodersen, D. E. (2018) “Structural basis for (p)ppGpp synthesis by the Staphylococcus aureus small alarmone synthetase RelP”, J Biol Chem, 293(9): 3254-64 (PubMed).

2017

Review on PIN domains, cover of Protein Science (Senissar et al., 2017)

Senissar, M., Manav, M. C., Brodersen, D. E. (2017) “Structural conservation of the PIN domain active site across all domains of life”, Protein Sci, 26(8):1474-1492 (PubMed).

* Bendtsen, K. L., Xu, K., Luckmann, M., Winther, K. S., Shah, S. A., Pedersen, C. N. S., and Brodersen, D. E. (2017) “Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo- palindromic protein motif and modulated by DNA binding”, Nucleic Acids Res, 45(5):2875-2886 (PubMed).

2016

Agerschou, E. D., Christiansen, G., Schafer, N. P., Madsen, D. J., Brodersen, D. E., Semsey, S., and Otzen, D. (2016) “The transcriptional regulator GalR self-assembles to form highly regular tubular structures”, Scientific Reports, 6:27672 (PubMed).

Romans-Fuertes, P., Sondergaard, T. E., Sandmann, M. I., Wollenberg, R. D., Nielsen, K. F., Hansen, F. T., Giese, H., Brodersen, D. E., and Sørensen, J. L. (2016) “Identification of the non-ribosomal peptide synthetase responsible for biosynthesis of the potential anti-cancer drug sansalvamide in Fusarium solani”, Curr Genet., 62(4):799-807 (PubMed).

Xu, K., Dedic, E., and Brodersen, D. E. (2016) “Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri”, Proteins, 84(7):892-899 (PubMed).

Sofos, N., Winkler, M. B., and Brodersen D. E. (2016) “RRM domain of human RBM7: purification, crystallization and structure determination”, Acta Crystallogr F Struct Biol Commun, 72(Pt 5):397-402 (PubMed).

Knudsen, M., Søndergaard, D., Tofting-Olesen, C., Hansen, F. T., Brodersen, D. E., Pedersen, C. N. (2016) “Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases”, Bioinformatics, 32(3):325-9 (PubMed).

2015

Gytz, H., Mohr, D., Seweryn, P., Yoshimura, Y., Kutlubaeva, Z., Dolman, F., Chelchessa, B., Chetverin, A. B., Mulder, F. A. A., Brodersen, D. E. and Knudsen, C. R. (2015) ” Structural basis for RNA-genome recognition during bacteriophage Qβ replication”, Nucleic Acids Res, 43(22):10893-906 (PubMed).

Seweryn, P., Van, L. B., Kjeldgaard, M., Russo, C. J., Passmore, L. A., Hove-Jensen, B., Jochimsen, B., Brodersen, D. E. (2015) “Structural insights into the bacterial carbon-phosphorus lyase machinery”, Nature, 525(7567): 68-72 (PubMed).

Sofos, N., Xu, K., Dedic, E., Brodersen, D. E. (2015) “Cut to the chase – Regulating translation through RNA cleavage”, Biochimie, 114: 10-17 (PubMed).

Hansen, F. T., Gardiner, D. M., Lysøe, E., Fuertes, P. R., Tudzynski, B., Wiemann, P., Sondergaard, T. E., Giese, H., Brodersen, D. E., Sørensen, J. L. (2015) “An update to polyketide synthase and non-ribosomal synthetase genes and nomenclature in Fusarium”, Fungal Genet Biol, 75: 20-29 (PubMed).

2014

Poulsen, J. B., Agerschou, E. D., Sanderson, L. E., Van, L. B., Boesen, T., and Brodersen, D. E. (2014) “Structural characterization and positioning of subunits in the THO complex by small-angle X-ray scattering (SAXS)”, PLoS One, 9(7): e103470 (PubMed).

Dedic, E., Seweryn, P., Jonstrup, A. T., Flygaard, R. K., Jensen, J. K., Fedosova, N. U., Hoffmann, S. V., Boesen, T., and Brodersen, D. E. (2014) “Rrp47p forms a heterodimer with yeast nuclear exosome component Rrp6p and restricts nuclease activity “, Biochem Biophys Res Commun, 450: 634–640 (PubMed).

Ribosome-dependent mRNA cleavage, cover of Cell (Neubauer et al., 2009)

Ribosome-dependent mRNA cleavage, cover of Cell (Neubauer et al., 2009)

Sørensen, J. L., Knudsen, M., Hansen, F. T., Olesen, C., Romans-Fuertes, P., Lee, T. V., Søndergaard, T. E., Pedersen, C. N. S., Brodersen, D. E., and Giese H. (2014) “Fungal NRPS-dependent siderophores: From function to prediction“ in “Fungal Secondary Metabolites”, Martín, J.-F., García-Estrada, C., Zeilinger, S. eds., Subscellular Biochemistry Series, Springer Verlag.

2013

Winther, K. S., Brodersen, D. E., Brown, A. K., Gerdes, K. (2013), “VapC of Mycobacterium tuberculosis Inhibits Translation by Endonucleolytic Cleavage of the Sarcin-Ricin Loop of 23S rRNA”, Nature Communications, e-pub ahead of print (PubMed).

Saguez, C., Gonzales, F. A., Schmid, M., Bøggild, A., Latrick, C. M., Malagon, F., Putnam, A., Sanderson, L., Jankowsky, E., Brodersen, D. E., Jensen, T. J. (2013) “Mutational analysis of the yeast RNA helicase Sub2p reveals conserved domains required for growth, mRNA export and genomic stability”, RNA, 19(10):1363-71 (PubMed).

Xu, K., Dedic, E., Cob-Cantal, P., Dienemann, C., Bøggild, A., Winther, K. S., Gerdes, K., and Brodersen, D. E. (2013), “Protein expression, crystallization, and preliminary x-ray crystallographic analysis of the isolated Shigella flexneri VapC toxin”, Acta Cryst. F, 69(Pt 7):762-5 (PubMed).

Brodersen, D. E., Andersen, G. R., and Andersen, C. B. F. (2013), ” MIMER: An Automated Spreadsheet-Based Crystallization Screening System”, Acta Cryst. F, 69(Pt 7):815-20 (PubMed).

2012

Bøggild, A. Sofos, N., Andersen, K. R., Feddersen, A., Easter, A. D., Passmore, L., and Brodersen, D. E. (2012), “The Crystal Structure of the Intact E. coli RelBE Toxin-Antitoxin Complex Provides the Structural Basis for Conditional Cooperativity”, Structure, 20(10):1641-8 (PubMed).

Feddersen, A., Dedic, E., Poulsen, E. G., Schmid, M., Van, L. B., Jensen, T. H., and Brodersen, D. E. (2012), “Saccharomyces cerevisiae Ngl3p is an active 3’-5’ exonuclease with a specificity towards poly-A RNA reminiscent of cellular deadenylases”, Nucleic Acids Res, 40(2): 837-46 (PubMed).

2011

Dienemann, C., Bøggild, A., and Brodersen, D. E. (2011), “Crystal structure of the VapBC toxin-antitoxin complex from Shigella flexnerii reveals a hetero-octameric DNA-binding assembly”, Journal of Molecular Biology, 414(5):713-22 (PubMed).

Poulsen, J. B., Andersen, K. R., Kjær, K. H., Durand, F., Faou, P., Vestergaard, A. L., Talbo, G. H., Hoogenraad, N., Brodersen, D. E., Justesen, J., and Martensen, J. (2011), ” Human 2′-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover”, Nucleic Acids Res, 39(9):3754-70 (PubMed).

2009

Neubauer, C., Gao, Y., Andersen, K. R., Dunham, C. D., Kelley, A. C., Hentschel, J., Gerdes, K., Ramakrishnan, V., and Brodersen, D. E. (2009) ” The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE”, Cell, 139(6): 1084-1095 (PubMed).

Bøggild, A., Overgaard, M., Valentin-Hansen, P., and Brodersen, D. E. (2009) ”Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA binding properties”, FEBS J, 276: 4328-39 (PubMed).

Andersen, K. R., Jonstrup, A. T., Van, L. B., and Brodersen, D. E. (2009) “The activity and selectivity of fission yeast Pop2p is affected by a high affinity for Zn2+ and Mn2+ in the active site”, RNA, 15: 850-861 (PubMed).

Lykke-Andersen, S., Brodersen, D. E., and Jensen, T. H. (2009) “Origins and activities of the eukaryotic exosome”, J. Cell Sci., 122(Pt 10): 1487-94 (PubMed).

2008

Assenholt, J., Mouaikel, J., Andersen, K. R., Brodersen, D. E., Libri, D., Jensen, T. H. (2008) “Exonucleolysis is required for nuclear mRNA quality control in yeast THO mutants”, RNA, 14(11): 2305-13 (PubMed).

Andersen, K. R., Jensen, T. H., Brodersen, D. E. (2008) “Take the “A” tail-quality control of ribosomal and transfer RNA”, Biochim. Biophys. Acta, 1779(9): 532-7 (PubMed).

2007

Nielsen, J. S., Bøggild, A., Andersen, C. B. F., Nielsen, G., Boysen, A., Brodersen, D. E., Valentin- Hansen, P. (2007) “An Hfq-like protein in archaea: Crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii”, RNA, 13(12): 2213-2223 (PubMed).

Jonstrup, A. T., Andersen, K. R., Van, L. B., Brodersen, D. E. (2007) “The 1.4 Å crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme”, Nucleic Acids Res, 35: 3153-3164 (PubMed).

2006

Midtgaard, S. F., Assenholt, J., Jonstrup, A. T., Van, L. B., Jensen, T. H., Brodersen, D. E. (2006) “Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain”, Proc Natl Acad Sci USA, 103(32):11898-903 (PubMed).

2005

Petry, S., Brodersen, D. E., Murphy, F. V. 4th, Dunham, C. M., Selmer, M., Tarry, M. J., Kelley, A. C., and Ramakrishnan, V. (2005) “Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon”, Cell, 123(7): 1255-1266 (PubMed).

Brodersen, D. E. and Nissen, P. (2005) “The Social Life of Ribosomal Proteins”, The FEBS Journal, 272(9): 2098-2108 (PubMed).

2003

Brodersen, D. E., Clemons, Jr., W. M., Carter, A. P., Wimberly, B. T., and Ramakrishnan, V. (2003) “Phasing the 30S ribosomal subunit structure”, Acta Cryst., D59: 2044-2050 (PubMed).

Pfister, P., Risch, M., Brodersen, D. E., and Böttger, E. C. (2003) “The role of 16S rRNA helix 44 in ribosomal resistance to hygromycin B”, Antimicrob. Agents Chemother., 47(5): 1496-502 (PubMed).

Brodersen, D. E. and Ramakrishnan, V. (2003) “Shape can be seductive”, Nature Struct. Biol., 10(2): 78-80 (PubMed).

2002

Brodersen, D. E., Clemons Jr., W. M., Carter, A. P., Wimberly, B. T., and Ramakrishnan, V. (2002) “Crystal Structure of the 30S Ribosomal Subunit from Thermus thermophilus: Structure of the Proteins and Their Interactions with 16S RNA”, J. Mol. Biol., 316(3):725-768 (PubMed).

2001

Brodersen, D. E., Carter, A. P., Clemons Jr., W. M., Morgan-Warren, R. J., Murphy IV, F. V., Ogle, J. M., Tarry, M. J., Wimberly, B. T. and Ramakrishnan, V. (2001). “Atomic Structures of the 30S Subunit and its Complexes with Ligands and Antibiotics”, Cold Spring Harbor Symp. Quant. Biol., 66: 17-32 (PubMed).

Clemons Jr., W. M., Brodersen, D. E., McCutcheon, J. P., May, J. L., Carter, A. P., Morgan-Warren, R. J., Wimberly, B. T., and Ramakrishnan, V. (2001) “Crystal Structure of the 30S Ribosomal Subunit from Thermus thermophilus: Purification, Crystallization and Structure Determination”, J. Mol. Biol., 310(4): 827-43 (PubMed).

Ogle, J. M., Brodersen, D. E., Clemons Jr., W. M., Tarry, M. J., Carter, A. P., and Ramakrishnan, V. (2001) “Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit”, Science, 292: 897- 902 (PubMed).

Carter, A. P., Clemons Jr., W. M., Brodersen, D. E., Morgan-Warren, R. J., Hartsch, T., Wimberly, B. T., and Ramakrishnan, V. (2001) “Crystal Structure of an Initiation Factor Bound to the 30S Ribosomal Subunit”, Science, 291: 498-501 (PubMed).

2000

Brodersen, D. E., Clemons Jr., W. M., Carter, A. P., Morgan-Warren, R. J., Wimberly, B. T., and Ramakrishnan, V. (2000) “The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit”, Cell, 103: 1143-1154 (PubMed).

Carter, A. P.*, Clemons Jr., W. M.*, Brodersen, D. E.*, Morgan-Warren, R. J.*, Wimberly, B. T., and Ramakrishnan, V. (2000) “Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics”, Nature, 407: 340-348 (PubMed).
*These authors contributed equally to the work

Wimberly Nature 2000

Crystal structure of the 30S ribosomal subunit, cover of Nature (Wimberly et al., 2000)

Wimberly, B. T.*, Brodersen, D. E.*, Clemons Jr., W. M.*, Morgan-Warren, R. J.*, Carter, A. P.*, Vonrhein, C., Hartsch, T., and Ramakrishnan, V. (2000) “Structure of the 30S ribosomal subunit”, Nature, 407: 327-339 (PubMed).
*These authors contributed equally to the work

Brodersen, D. E., La Fortelle, E. de, Vonrhein, C., Bricogne, G., Nyborg, J., and Kjeldgaard, M. (2000) “Applications of single wavelength anomalous dispersion at high and atomic resolution”, Acta Cryst., D56: 431-441 (PubMed). Erratum in Acta Cryst., D62: 1102 (2006).

Brodersen, D.E., Jenner, L. B., Andersen, G. R., and Nyborg, J. (1999) “XAct: A program for construction, automated setup, and bookkeeping of crystallisation experiments”, J. Appl. Cryst., 32(Pt 5): 1012-1016 (not available in PubMed, direct link).

Brodersen, D.E. and Kjeldgaard, M. (1999) “Structural investigations of calcium and zinc binding in proteins”, Sci. Prog., 82(4): 295-312 (PubMed).

Brodersen, D. E., Nyborg, J., and Kjeldgaard, M. (1999) “Zinc-Binding site of an S100 protein revealed. Two crystal structures of Ca2+-bound human psoriasin (S100A7) in the Zn2+-loaded and Zn2+-free states”, Biochemistry, 38(6): 1695-1704 (PubMed).

Brodersen, D. E., Etzerodt, M., Madsen, P., Thøgersen, H. C., Celis, J. E., Nyborg, J., and Kjeldgaard, M. (1998) “EF-hands at atomic resolution: The structure of human psoriasin (S100A7) solved by MAD phasing”, Structure, 6: 477-489 (PubMed).

Merli, A., Brodersen, D. E., Morini, B., Chen, Z.-W., Durley, R. C. E., Scott Mathews, F., Davidson, V. L., and Rossi, G. L. (1996) ”Enzymatic and electron transfer activities in crystalline protein complexes”, J. Biol. Chem., 271(16): 9177-9180 (PubMed).