Publications

2018

Bock LV, Kolar MH, Grubmüller H (2018) Molecular simulations of the ribosome and associated translation factors. Curr. Opin. Struct. Biol. 49, 27-35

2017

Huter P, Arenz S, Bock LV, Graf M, Frister JO, Heuer A, Peil L, Starosta AL, Wohlgemuth I, Peske F, Nováček J, Berninghausen O, Grubmüller H, Tenson T, Beckmann R, Rodnina MV, Vaiana AC, Wilson DN. (2017) Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. Mol Cell 68: 515-527

Florin T, Maracci C, Graf M, Karki P, Klepacki D, Berninghausen O, Beckmann R, Vázquez-Laslop N, Wilson DN, Rodnina MV, Mankin AS (2017) An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome. Nat Struct Mol Biol. 24 :752-757

Huter P, Müller C, Arenz S, Beckert B, Wilson DN. (2017) Structural Basis for Ribosome Rescue in Bacteria. Trends Biochem Sci. Aug;42(8): 669-680

Su T, Cheng J, Sohmen D, Hedman R, Berninghausen O, von Heijne G, Wilson DN, Beckmann R. (2017) The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. Elife. May 30; 6

Graf M, Mardirossian M, Nguyen F, Seefeldt AC, Guichard G, Scocchi M, Innis CA, Wilson DN. (2017) Proline-rich antimicrobial peptides targeting protein synthesis. Nat Prod Rep. 34: 702-711

Graf M, Arenz S, Huter P, Dönhöfer A, Novácek J, Wilson DN. (2017) Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions. Nucleic Acids Res. 45: 2887-2896

Caliskan N, Wohlgemuth I, Korniy N, Pearson M, Peske F, Rodnina MV (2017) Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA. Mol Cell 18: 558-567

Rodnina MV, Fischer N, Maracci C, Stark H (2017) Ribosome dynamics during decoding. Philos Trans R Soc Lond Biol Sci 372: 1716

Kirchner S, Cai Z, Rauscher R, Kastelic N, Anding M, Czech A, Kleizen B, Ostedgaard LS, Braakman I, Sheppard DN, Ignatova Z (2017) Alteration of protein function by a silent polymorphism linked to tRNA abundance. PLOS Biology 15, e2000779

Wellner K, Czech A, Ignatova Z., Betat H, Mörl M. (2017), Examining tRNA 3'-ends in Escherichia coli: A teamwork between CCA-adding enzyme, RNaseT and RNaseR. RNA, in press

Ignatova Z., Narberhaus F (2017) systematic probing of the bacterial RNA structurome to reveal new functions. Curr. Opin. Microbiol. 36, 14-19

Bartholomäus A, Del Campo C, Ignatova Z. (2016) Mapping the non-standardized biases of ribosome profiling, Biol. Chem. 397, 23-35

Ferro I, Chelysheva I, Ignatova Z. (2017) Competition for amino acids flux among translation, growth and detoxification in bacteria. RNA Biol. 14, 1-4

Kater L., Thoms M., Barrio-Garcia C., Cheng J., Ismail S., Ahmed Y.L., Bange G., Kressler D., Berninghausen O., Sinning I., Hurt E., Beckmann R. (2017) Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Cell 171:1599-1610

Heuer A., Thomson E., Schmidt C., Berninghausen O., Becker T., Hurt E.,2, Beckmann R. (2017) Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae. Elife 20: 6

Matsuo .Y, Ikeuchi K., Saeki Y., Iwasaki S., Schmidt C., Udagawa T., Sato F., Tsuchiya H., Becker T., Tanaka K., Ingolia N.T., Beckmann R., Inada T. (2017) Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nat Commun. 8: 159

Yamashita Y., Takamatsu S., Glasbrenner M., Becker T., Naito S., Beckmann R. (2017) Sucrose sensing through nascent peptide-meditated ribosome stalling at the stop codon of Arabidopsis bZIP11 uORF2. FEBS Lett. 591: 1266-1277

Heuer A., Gerovac M., Schmidt .C, Trowitzsch S., Preis A., Kötter P., Berninghausen O., Becker T., Beckmann R., Tampé R. (2017) Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation. Nat Struct Mol Biol. 24: 453-460

Cheng J., Kellner N., Berninghausen O., Hurt E., Beckmann R. (2017) 3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage. Nat Struct Mol Biol. 24: 954-964

Nilsson O.B., Nickson A.A., Hollins J.J., Wickles S., Steward A., Beckmann R., von Heijne G., Clarke J. (2017) Cotranslational folding of spectrin domains via partially structured states.Nat Struct Mol Biol. 24: 221-225

Su T., Cheng J., Sohmen D., Hedman R., Berninghausen O., von Heijne .G, Wilson D.N., Beckmann R. (2017) The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. Elife. 30; 6

Huter P, Müller C, Beckert B, Arenz S, Berninghausen O, Beckmann R, Wilson DN (2017) Structural basis for ArfA-RF2-mediated translation termination on mRNAs lacking stop codons. Nature

Thommen M, Holtkamp W, Rodnina MV (2017) Co-translational protein folding: progress and methods Curr Opin Struct Biol.

2016

Marino J., von Heijne G., Beckmann R. (2016) Small protein domains fold inside the ribosome exit tunnel. FEBS Lett. 590: 655-60

Deeng J., Chan K.Y., van der Sluis E.O., Berninghausen O., Han W., Gumbart J., Schulten K., Beatrix B., Beckmann R. (2016) Dynamic Behavior of Trigger Factor on the Ribosome. J Mol Biol. 428: 3588-602

Kornprobst M., Turk M., Kellner N., Cheng J., Flemming D., Koš-Braun I., Koš M., Thoms M., Berninghausen O., Beckmann R., Hurt E. (2016) Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. Cell. 166: 380-393

Kiosze-Becker K., Ori A., Gerovac M., Heuer A., Nürenberg-Goloub E., Rashid U.J., Becker T., Beckmann R., Beck M., Tampé R. (2016) Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry. Nat Commun. 8: 13248

ScSchmidt C., Kowalinski E., Shanmuganathan V., Defenouillère Q., Braunger K., Heuer A., Pech M., Namane A., Berninghausen O., Fromont-Racine M., Jacquier A., Conti E., Becker T., Beckmann R. (2016) The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Science 354: 1431-1433

Buhr F, Jha S, Thommen M, Mittelstät J, Kutz F, Schwalbe H, Rodnina MV, Komar AA (2016) Synonymous codons direct cotranslational folding toward different protein conformations. Mol Cell 61:341-351

Rodnina MV (2016) The ribosome in action: Tuning of translational efficiency and protein folding Protein Sci 25: 1390-406

Exner MP, Kuenzl T, Schwagerus S, To TTT, Ouyang Z, Hoesl MG, Lensen MC, Hackenberger CPR, Panke S, Budisa N (2016) Design of an S-Allylcysteine in situ production and incorporation system based on a novel pyrrolysyl-tRNA synthetase variant. ChemBioChem, in press

Kubyshkin V, Budisa N (2016) cis-trans-Amide isomerism of the 3,4-dehydroproline residue, the 'unpuckered' proline. Beilstein J Org Chem 12: 589-593

Kubyshkin V, Durkin PM, Budisa N (2016) Energetic contribution to both acidity and conformational stability in the peptide models New J Chem 40: 5209-5220

Jaric J, Budisa N (2016) Design of orthogonal pairs for protein translation: selection systems for genetically encoding noncanonical amino acids in E coli In: Hydrocarbon and Lipid Microbiology Protocols: Cultivation Springer Protocols Handbooks, (ISBN 978-3-662-45179-3), Springer, pp 71-82127

Arenz S, Wilson DN (2016) Bacterial Protein Synthesis as a Target for Antibiotic Inhibition. Cold Spring Harb Perspect Med, 6(9)

Arenz S, Juette MF, Graf M, Nguyen F, Huter P, Polikanov YS, Blanchard SC, Wilson DN (2016) Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome. Proc Natl Acad Sci USA, 113:7527-32

Arenz S, Abdelshahid M, Sohmen D, Payoe R, Starosta AL, Berninghausen O, Hauryliuk V, Beckmann R, Wilson DN (2016) The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis. Nucleic Acids Res. 44:6471-81.

Wilson DN, Arenz S, Beckmann R (2016) Translation regulation via nascent polypeptide-mediated ribosome stalling. Current Opinion in Structural Biology 2016, 37:123-133

Seefeldt CA, Graf M, Pérébaskine N, Nguyen F, Arenz S, Mardirossian M, Scocchi M, Wilson DN, Innis CA (2016) Structure of the mammalian antimicrobial peptide Bac7(1- 16) bound within the exit tunnel of a bacterial ribosome. Nucl Acids Res., 44:2429-38

Schmidt C, Becker T, Heuer A, Braunger K, Shanmuganathan V, Pech M, Berninghausen O, Wilson DN, Beckmann R (2016) Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. Nucl Acids Res., 44:1944-51

Lassak J, Wilson DN, Jung K (2016) Stall no more at polyproline stretches with the translation factors EF-P and IF-5A. Mol Microbiol. 99, 219-235

Arenz S, Wilson DN (2016) Blast from the Past: Reassessing Forgotten Translation Inhibitors, Antibiotic Selectivity, and Resistance Mechanisms to Aid Drug Development. Molecular Cell. 61:3-14

Rodnina MV, Wintermeyer W. (2016) Protein Elongation, Co-translational Folding and Targeting. J Mol Biol 428: 2165-2185

Katoh T, Wohlgemuth I, Nagano M, Rodnina MV, Suga H. (2016) Essential structural elements in tRNA(Pro) for EF-P-mediated alleviation of translation stalling. Nat Commun 7:11657

Fischer N, Neumann P, Bock lV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H (2016)The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature

Arenz S, Bock LV, Graf M, Innis CA, Beckmann R, Grubmüller H, Vaiana AC, Wilson DN (2016) A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest. Nature Comm.

Bartholomäus A, Fedyunin I, Feist P, Sin C, Zhang G, Valleriani A, Ignatova Z (2016) Bacteria differently regulate mRNA abundance to specifically respond to various stresses. Phil. Transact A 374.: 2063

Avcilar-Kucukgoze I, Bartholomäus A, Cordero Varela JA, Kaml RF, Neubauer P, Budisa N, Ignatova Z (2016) Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli. Nucl. Acids. Res. 44: 8324-8334

Saffert P, Adamla F, Schieweck R, Atkins JF, Ignatova Z (2016) An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting. J Biol Chem. 291:18505-13

Gorochowski TE, Avcilar-Kucukgoze I, Bovenberg RA, Roubos JA, Ignatova Z (2016) A minimal model of ribosome allocation dynamics captures trade-offs in expression between endogenous and synthetic genes. ACS Synth Biol. 5:710-720

2015

Doerfel LK, Wohlgemuth I, Kubyshkin V, Starosta AL, Wilson DN, Budisa N, Rodnina MV (2015) Entropic contribution of elongation factor P to proline positioning at the catalytic center of the ribosome. J Am Chem Soc. 137:12997-3006

Beckert B, Kedrov A, Sohmen D, Kempf G, Wild K, Sinning I, Stahlberg H, Wilson DN, Beckmann R (2015) Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions. Nat Struct Mol Biol. 22:767-73

Polikanov YS, Starosta AL, Juette MF, Altman RB, Terry DS, Lu W, Burnett BJ, Dinos G, Reynolds K, Blanchard SC, Steitz TA, Wilson DN (2015) Distinct tRNA accommodation intermediates observed on the ribosome with the antibiotics hygromycin A and A201A. Molecular Cell, 58:832-44

Seefeldt AC, Nguyen F, Antunes S, Pérébaskine N, Graf M, Arenz S, Inampudi KK, Douat C, Guichard G, Wilson DN, Innis CA (2015) The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex. Nat. Struct. Mol Biol. 22:470-5

Sohmen D, Chiba S, Shimokawa-Chiba N, Innis CA, Berninghausen O, Beckmann R, Ito K, Wilson DN (2015) Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Nature communications, 6:6941

Byrgazov K, Grishkovskaya I, Arenz S, Coudevylle N, Temmel H, Wilson DN, Djinovic-Carugo K and Moll I (2015) Structural basis for the interaction of protein S1 with the Escherichia coli ribosome. Nucl Acids Res., 43:661-73

Holtkamp W, Kokic G, Jäger M, Mittelstaet J, Komar AA, Rodnina MV (2015) Cotranslational protein folding on the ribosome monitored in real time. Science 350: 1104-1107

Gorochowski TE, Ignatova Z, Bovenberg RA, Roubos JA (2015) Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate. Nucleic Acids Res. 43: 3022-32

Del Campo C, Bartholomäus A, Fedyunin I, Ignatova Z (2015) Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function. PLoS Genet. 11, e1005613

Ferro I, Ignatova Z (2015) Quantifying the 'escapers' among RNA species. Biochem. Soc. Trans. 43: 1215-20

Rauscher R, Ignatova Z (2015) Tuning innate immunity by translation, Biochem. Soc. Trans. 43: 1247-52

Del Campo C, Ignatova Z (2015) Probing dimensionality beyond the linear sequence of mRNA. Curr Genet. 62, 331-4

Al Toma RS, Kuthning A, Exner MP, Denisiuk A, Ziegler J, Budisa N, Süssmuth RD (2015) Site-Directed and Global Incorporation of Orthogonal and Isostructural Noncanonical Amino Acids into the Ribosomal Lasso Peptide Capistruin. ChemBioChem 16: 503-509.

Arenz S, Nguyen F, Beckmann R, Wilson DN (2015) Cryo-EM structure of the tetracycline resistance protein TetM in complex with a translating ribosome at 3.9 Å resolution. Proc. Natl Acad. Sci. USA, 112:5401-6

Dietz D, Kubyshkin V, Budisa N (2015) Applying γ-substituted prolines in the foldon peptide: polarity contradicts preorganization. ChemBioChem 16: 403-406.

Fischer N, Neumann P, Konevega AL, Bock LV, Ficner R, Rodnina MV, Stark H (2015) Structure of the E. coli ribosome-EF-Tu complex at < 3 Å resolution by C_s-corrected cryo-EM. Nature, in press.

Kirchner S, Ignatova Z (2015) Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet. 16:98-112.

Sohmen D, Chiba S, Shimokawa-Chiba N, Innis CA, Berninghausen O, Beckmann R, Ito K and Wilson DN (2015) Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Nature Commun., in press.

Hoesl MG, Oehm S, Durkin P, Darmon E, Peil L, Aerni H-R, Rappsilber J, Rinehart J, Leach D, Söll D, Budisa N (2015) Chemical evolution of a bacterial proteome Angew Chem Int Ed Engl 54: 10030-10034

2014

Arenz S, Meydan S, Starosta AL, Berninghausen O, Beckmann R, Vázquez-Laslop N and Wilson DN (2014) Drug Sensing by the Ribosome Induces Translational Arrest via Active Site Perturbation. Mol Cell 6: 446-52.

Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, Lafontaine DL, Lindahl L, Liljas A, Lipton JM, McAlear MA, Moore PB, Noller HF, Ortega J, Panse VG, Ramakrishnan V, Spahn CM, Steitz TA, Tchorzewski M, Tollervey D, Warren AJ, Williamson JR, Wilson D, Yonath A and Yusupov M (2014) A new system for naming ribosomal proteins. Curr Opin Struct Biol 24:165-189.

Bohlke N and Budisa N (2014) Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion. FEMS Microbiol Lett. 351: 133-144.

Byrgazov K, Grishkovskaya I, Arenz S, Coudevylle N, Temmel H, Wilson DN, Djinovic-Carugo K and Moll I (2014) Structural basis for the interaction of protein S1 with the Escherichia coli ribosome. Nucleic acids Res. 43:661-73.

Gloge F, Becker AH, Kramer G and Bukau B (2014) Co-translational mechanisms of protein maturation Curr Opin Struct Biol 24: 24-33.

Ma Y, Biava H, Contestabile R, Budisa N and di Salvo ML (2014) Coupling bioorthogonal bhemistries with artificial metabolism. Molecules19: 1004-1022.

Maracci C, Peske F, Dannies E, Pohl C and Rodnina MV (2014) Ribosome-induced tuning of GTP hydrolysis by a translational GTPase. Proc Natl Acad Sci USA 111: 14418-23

Nguyen F, Starosta AL, Arenz S, Sohmen D, Dönhöfer A and Wilson DN (2014) Tetracycline antibiotics and resistance mechanisms. Biol Chem 395: 16900-5.

Preis A, Heuer A, Barrio-Garcia C, Hauser A, Eyler DE, Berninghausen O, Green R, Becker T, Beckmann R (2014) Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1. Cell Rep. 8:59-65.

Puri P, Wetzel C, Saffert P, Gaston KW, Russell SP, van der Vlies P, Zhang G, Limbach P, Ignatova Z and Poolman B (2014) Systematic identification of tRNAome and its dynamics in Lactococcus lactis. Mol. Microbiol. 93: 944-956.

Rudorf S, Thommen M, Rodnina MV, Lipowsky R (2014) Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro. PLoS Comput Biol. 10:e1003909.

Starosta AL, Lassak J, Peil L, Atkinson GC, Woolstenhulme CJ, Virumäe K, Buskirk A, Tenson T, Remme J, Jung K, Wilson DN (2014) A conserved proline triplet in Val-tRNA synthetase and the origin of elongation factor P. Cell reports 9:476-83.

Starosta AL, Lassak J, Peil L, Atkinson GC, Virumäe K, Tenson T, Remme J, Jung K, Wilson DN (2014) Translational stalling at polyproline-stretches is modulated by the sequence context upstream of the stall site. Nucl Acids Res 42:10711-9.

Starosta AL, Lassak J, Jung K and Wilson DN (2014) The bacterial translation stress response. FEMS Microbiol Rev 38:1172-201.

Yamamoto H, Unbehaun A, Loerke J, Behrmann E, Collier M, Bürger J, Mielke T and Spahn CMT (2014) Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV IRES RNA. Nature Struct Mol Biol 21: 721-7.

Yamamoto H, Qin Y, Achenbach J, Li CM, Kijek J, Spahn CMT and Nierhaus KH (2014) EF-G and EF4: translocation and back-translocation on the bacterial ribosome. Nature Rev Microbiol 12: 89-100.

2013

Anger AM, Armache JP, Berninghausen O, Habeck M, Subklewe M, Wilson DN and Beckmann R (2013) Structures of the human and Drosophila 80S ribosome Nature 497: 80-85.

Becker AH, Oh E, Weissman JS, Kramer G and Bukau B (2013) Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes Nature Prot. 8: 2212-39.

Blau C and Grubmüller H (2013) Fast contact search in bio-molecular ensemble data. Comp Phys Commun 184: 2856–2859

Bock LV, Blau C, Schröder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC and Grubmüller H (2013) Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol. 20:1390-6.

Czech A, Wende S, Mörl M, Pan T and Ignatova Z (2013) Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress. PLoS Genet. 9: e1003767.

Doerfel LK, Wohlgemuth I, Kothe C, Peske F, Urlaub H and Rodnina MV (2013) EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science 339: 85-88.

Doerfel LK and Rodnina MV (2013) Elongation factor P: Function and effects on bacterial fitness Biopolymers 99: 837-845.

Jenner L, Starosta AL ,Terry DS, Mikolajka A, Filonava L, Yusupov M, Blanchard SC, Wilson DN and Yusupova G (2013) Structural basis for potent inhibitory activity of the antibiotic tigecycline during protein synthesis. Proc Natl Acad Sci USA 110: 3812-6

Luckoszek R, Mueller-Roeber B and Ignatova Z (2013) Interplay between pol II and pol II-assisted expression of overlapping genes. FEBS Lett. 587: 3692-3695.

Mittelstaet J, Konevega AL and Rodnina MV (2013) A kinetic safety gate controlling the delivery of unnatural amino acids to the ribosome J Am Chem Soc 135: 17031-17038.

Ramrath DJ, Lancaster L, Sprink T, Mielke T, Loerke J, Noller HF and Spahn CMT (2013) Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation. Proc Natl Acad Sci USA 110: 20964-9.

2012

Dönhöfer A, Franckenberg S, Wickles S, Berninghausen O, Beckmann R and Wilson DN (2012) Structural basis for TetM-mediated tetracycline resistance. Proc Natl Acad Sci USA 109: 16900-5.

PIs from this Research Unit (FOR 1805) are highlighted in bold