Rodnina, Marina V.

[["dc.bibliographiccitation.firstpage","531"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Molecular Cell"],["dc.bibliographiccitation.lastpage","540"],["dc.bibliographiccitation.volume","56"],["dc.contributor.author","Polikanov, Yury S."],["dc.contributor.author","Osterman, Ilya A."],["dc.contributor.author","Szal, Teresa"],["dc.contributor.author","Tashlitsky, Vadim N."],["dc.contributor.author","Serebryakova, Marina V."],["dc.contributor.author","Kusochek, Pavel"],["dc.contributor.author","Bulkley, David"],["dc.contributor.author","Malanicheva, Irina A."],["dc.contributor.author","Efimenko, Tatyana A."],["dc.contributor.author","Efremenkova, Olga V."],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Shaw, Karen J."],["dc.contributor.author","Bogdanov, Alexey A."],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Dontsova, Olga A."],["dc.contributor.author","Mankin, Alexander S."],["dc.contributor.author","Steitz, Thomas A."],["dc.contributor.author","Sergiev, Petr V."],["dc.date.accessioned","2017-09-07T11:45:24Z"],["dc.date.available","2017-09-07T11:45:24Z"],["dc.date.issued","2014"],["dc.description.abstract","We demonstrate that the antibiotic amicoumacin A (AMI) is a potent inhibitor of protein synthesis. Resistance mutations in helix 24 of the 16S rRNA mapped the AMI binding site to the small ribosomal subunit. The crystal structure of bacterial ribosome in complex with AMI solved at 2.4 angstrom resolution revealed that the antibiotic makes contacts with universally conserved nucleotides of 16S rRNA in the E site and the mRNA backbone. Simultaneous interactions of AMI with 16S rRNA and mRNA and the in vivo experimental evidence suggest that it may inhibit the progression of the ribosome along mRNA. Consistent with this proposal, binding of AMI interferes with translocation in vitro. The inhibitory action of AMI can be partly compensated by mutations in the translation elongation factor G."],["dc.identifier.doi","10.1016/j.molcel.2014.09.020"],["dc.identifier.gro","3142016"],["dc.identifier.isi","000345502200009"],["dc.identifier.pmid","25306919"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/3612"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1097-4164"],["dc.relation.issn","1097-2765"],["dc.title","Amicoumacin A Inhibits Translation by Stabilizing mRNA Interaction with the Ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","The FEBS journal / Supplement"],["dc.bibliographiccitation.volume","282"],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","Maksimova, E."],["dc.contributor.author","Kasatsky, Pavel"],["dc.contributor.author","Makhno, V. I."],["dc.contributor.author","Osterman, Ilya A."],["dc.contributor.author","Dontsova, Olga A."],["dc.contributor.author","Sergiev, Petr V."],["dc.contributor.author","Konevega, Andrey L."],["dc.date.accessioned","2017-09-07T11:45:52Z"],["dc.date.available","2017-09-07T11:45:52Z"],["dc.date.issued","2015"],["dc.format.extent","371"],["dc.identifier.gro","3145548"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/3258"],["dc.notes.intern","lifescience"],["dc.notes.status","public"],["dc.notes.submitter","oschaef1"],["dc.publisher","Wiley-Blackwell"],["dc.relation.conference","40th Congress of the Federation of European Biochemical Societies (FEBS) - The Biochemical Basis of Life"],["dc.relation.eissn","1742-4658"],["dc.relation.eventend","2015-07-09"],["dc.relation.eventlocation","Berlin"],["dc.relation.eventstart","2015-07-04"],["dc.relation.issn","1742-464X"],["dc.title","Inhibition of translation elongation by antibiotic amicoumacin A"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1848"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","RNA"],["dc.bibliographiccitation.lastpage","1853"],["dc.bibliographiccitation.volume","16"],["dc.contributor.author","Burakovsky, Dmitry E."],["dc.contributor.author","Sergiev, Petr V."],["dc.contributor.author","Steblyanko, Maria A."],["dc.contributor.author","Kubarenko, Andriy V."],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Bogdanov, Alexey A."],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Dontsova, Olga A."],["dc.date.accessioned","2017-09-07T11:45:20Z"],["dc.date.available","2017-09-07T11:45:20Z"],["dc.date.issued","2010"],["dc.description.abstract","During protein synthesis, aminoacyl-tRNA (aa-tRNA) and release factors 1 and 2 (RF1 and RF2) have to bind at the catalytic center of the ribosome on the 50S subunit where they take part in peptide bond formation or peptidyl-tRNA hydrolysis, respectively. Computer simulations of aa-tRNA movement into the catalytic site (accommodation) suggested that three nucleotides of 23S rRNA, U2492, C2556, and C2573, form a \"gate\" at which aa-tRNA movement into the A site is retarded. Here we examined the role of nucleotides C2573 of 23S rRNA, a part of the putative accommodation gate, and of the neighboring A2572 for aa-tRNA binding followed by peptide bond formation and for the RF2-dependent peptide release. Mutations at the two positions did not affect aa-tRNA accommodation, peptide bond formation, or the fidelity of aa-tRNA selection, but impaired RF2-catalyzed peptide release. The data suggest that the ribosome is a robust machine that allows rapid aa-tRNA accommodation despite the defects at the accommodation gate. In comparison, peptide release by RF2 appears more sensitive to these mutations, due to slower accommodation of the factor or effects on RF2 positioning in the A site."],["dc.identifier.doi","10.1261/rna.2185710"],["dc.identifier.gro","3142870"],["dc.identifier.isi","000281003900013"],["dc.identifier.pmid","20668033"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/321"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1355-8382"],["dc.title","Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1073"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","The EMBO journal"],["dc.bibliographiccitation.lastpage","1085"],["dc.bibliographiccitation.volume","33"],["dc.contributor.author","Holtkamp, Wolf"],["dc.contributor.author","Cunha, Carlos E. da"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2018-01-26T06:04:53Z"],["dc.date.available","2018-01-26T06:04:53Z"],["dc.date.issued","2014"],["dc.description.abstract","Elongation factor G (EF-G) promotes the movement of two tRNAs and the mRNA through the ribosome in each cycle of peptide elongation. During translocation, the tRNAs transiently occupy intermediate positions on both small (30S) and large (50S) ribosomal subunits. How EF-G and GTP hydrolysis control these movements is still unclear. We used fluorescence labels that specifically monitor movements on either 30S or 50S subunits in combination with EF-G mutants and translocation-specific antibiotics to investigate timing and energetics of translocation. We show that EF-G-GTP facilitates synchronous movements of peptidyl-tRNA on the two subunits into an early post-translocation state, which resembles a chimeric state identified by structural studies. EF-G binding without GTP hydrolysis promotes only partial tRNA movement on the 50S subunit. However, rapid 30S translocation and the concomitant completion of 50S translocation require GTP hydrolysis and a functional domain 4 of EF-G. Our results reveal two distinct modes for utilizing the energy of EF-G binding and GTP hydrolysis and suggest that coupling of GTP hydrolysis to translocation is mediated through rearrangements of the 30S subunit."],["dc.identifier.doi","10.1002/embj.201387465"],["dc.identifier.pmid","24614227"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11834"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1460-2075"],["dc.title","GTP hydrolysis by EF-G synchronizes tRNA movement on small and large ribosomal subunits"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","16924"],["dc.bibliographiccitation.issue","44"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","16927"],["dc.bibliographiccitation.volume","105"],["dc.contributor.author","Julián, Patricia"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Scheres, Sjors H. W."],["dc.contributor.author","Lazaro, Melisa"],["dc.contributor.author","Gil, David"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Valle, Mikel"],["dc.date.accessioned","2017-09-07T11:48:09Z"],["dc.date.available","2017-09-07T11:48:09Z"],["dc.date.issued","2008"],["dc.description.abstract","During protein synthesis, tRNAs and mRNA move through the ribosome between aminoacyl (A), peptidyl (P), and exit (E) sites of the ribosome in a process called translocation. Translocation is accompanied by the displacement of the tRNAs on the large ribosomal subunit toward the hybrid A/P and P/E states and by a rotational movement (ratchet) of the ribosomal subunits relative to one another. So far, the structure of the ratcheted state has been observed only when translation factors were bound to the ribosome. Using cryo-electron microscopy and classification, we show here that ribosomes can spontaneously adopt a ratcheted conformation with tRNAs in their hybrid states. The peptidyl-tRNA molecule in the A/P state, which is visualized here, is not distorted compared with the A/A state except for slight adjustments of its acceptor end, suggesting that the displacement of the A-site tRNA on the SOS subunit is passive and is induced by the 30S subunit rotation. Simultaneous subunit ratchet and formation of the tRNA hybrid states precede and may promote the subsequent rapid and coordinated tRNA translocation on the 30S subunit catalyzed by elongation factor G."],["dc.identifier.doi","10.1073/pnas.0809587105"],["dc.identifier.gro","3143212"],["dc.identifier.isi","000260913800025"],["dc.identifier.pmid","18971332"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/701"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0027-8424"],["dc.title","Structure of ratcheted ribosomes with tRNAs in hybrid states"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","80"],["dc.bibliographiccitation.issue","7631"],["dc.bibliographiccitation.journal","Nature"],["dc.bibliographiccitation.lastpage","85"],["dc.bibliographiccitation.volume","540"],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Maracci, Cristina"],["dc.contributor.author","Wang, Zhe"],["dc.contributor.author","Paleskava, Alena"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Schröder, Gunnar F."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Stark, Holger"],["dc.date.accessioned","2017-09-07T11:44:31Z"],["dc.date.available","2017-09-07T11:44:31Z"],["dc.date.issued","2016"],["dc.description.abstract","In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA(Sec)) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA(Sec) recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNA(Sec) binding by SelB and show large-scale rearrangements of Sec-tRNA(Sec). Upon initial binding of SelB-Sec-tRNA(Sec) to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNA(Sec) covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNA(Sec) away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases."],["dc.identifier.doi","10.1038/nature20560"],["dc.identifier.gro","3141595"],["dc.identifier.isi","000388916600051"],["dc.identifier.pmid","27842381"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/6"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1476-4687"],["dc.relation.issn","0028-0836"],["dc.title","The pathway to GTPase activation of elongation factor SelB on the ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","8158"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Journal of biological chemistry"],["dc.bibliographiccitation.lastpage","8164"],["dc.bibliographiccitation.volume","286"],["dc.contributor.author","Mittelstaet, Joerg"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2017-09-07T11:44:20Z"],["dc.date.available","2017-09-07T11:44:20Z"],["dc.date.issued","2011"],["dc.description.abstract","The accurate decoding of the genetic information by the ribosome relies on the communication between the decoding center of the ribosome, where the tRNA anticodon interacts with the codon, and the GTPase center of EF-Tu, where GTP hydrolysis takes place. In the A/T state of decoding, the tRNA undergoes a large conformational change that results in a more open, distorted tRNA structure. Here we use a real-time transient fluorescence quenching approach to monitor the timing and the extent of the tRNA distortion upon reading cognate or near-cognate codons. The tRNA is distorted upon codon recognition and remains in that conformation until the tRNA is released from EF-Tu, although the extent of distortion gradually changes upon transition from the pre- to the post-hydrolysis steps of decoding. The timing and extent of the rearrangement is similar on cognate and near-cognate codons, suggesting that the tRNA distortion alone does not provide a specific switch for the preferential activation of GTP hydrolysis on the cognate codon. Thus, although the tRNA plays an active role in signal transmission between the decoding and GTPase centers, other regulators of signaling must be involved."],["dc.identifier.doi","10.1074/jbc.M110.210021"],["dc.identifier.gro","3142762"],["dc.identifier.isi","000288013300046"],["dc.identifier.pmid","21212264"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/201"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Deutsche Forschungsgemeinschaft"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0021-9258"],["dc.title","Distortion of tRNA upon Near-cognate Codon Recognition on the Ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.lastpage","30"],["dc.bibliographiccitation.volume","430"],["dc.contributor.author","Milon, Pohl"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Fabbretti, Attilio"],["dc.contributor.author","Gualerzi, Claudio O."],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.editor","Ziegler, Christine"],["dc.date.accessioned","2017-09-07T11:49:53Z"],["dc.date.available","2017-09-07T11:49:53Z"],["dc.date.issued","2007"],["dc.description.abstract","Initiation of mRNA translation in prokaryotes requires the small ribosomat subunit (30S), initiator fMet-tRNA(fMet), three initiation factors, IF1, IF2, and IF3, and the large ribosomal subunit (50S). During initiation, the 30S subunit, in a complex with IF3, binds mRNA, IF1, IF2-GTP, and fMet-tRNA(fMet) to form a 30S initiation complex which then recruits the 50S subunit to yield a 70S initiation complex, while the initiation factors are released. Here we describe a transient kinetic approach to study the timing of elemental steps Of 30S initiation complex formation, 50S subunit joining, and the dissociation of the initiation factors from the 70S initiation complex. Labeling of ribosomal subunits, fMet-tRNA(fMet), mRNA, and initiation factors with fluorescent reporter groups allows for the direct observation of the formation or dissociation of complexes by monitoring changes in the fluorescence of single dyes or fluorescence resonance energy transfer (FRET) between two fluorophores. Subunit joining was monitored by light scattering or by FRET between dyes attached to the ribosomat subunits. The kinetics of chemical steps, that is, GTP hydrolysis by IF2 and peptide bond formation following the binding of aminoacyl-tRNA to the 70S initiation complex, were measured by the quench-ftow technique. The methods described here are based on results obtained with initiation components from Escherichia coli but can be adopted for mechanistic studies of initiation in other prokaryotic or eukaryotic systems."],["dc.identifier.doi","10.1016/S0076-6879(07)30001-3"],["dc.identifier.gro","3143569"],["dc.identifier.isi","000250402400001"],["dc.identifier.pmid","17913632"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1097"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Elsevier Academic Press Inc"],["dc.publisher.place","San diego"],["dc.relation.crisseries","Methods in Enzymology"],["dc.relation.isbn","978-0-12-373969-8"],["dc.relation.ispartof","Methods in enzymology"],["dc.relation.ispartofseries","Methods in Enzymology"],["dc.relation.issn","0076-6879"],["dc.title","Transient kinetics, fluorescence, and fret in studies of initiation of translation in bacteria"],["dc.type","book_chapter"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","712"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Molecular Cell"],["dc.bibliographiccitation.lastpage","720"],["dc.bibliographiccitation.volume","30"],["dc.contributor.author","Milon, Pohl"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Gualerzi, Claudio O."],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2017-09-07T11:48:17Z"],["dc.date.available","2017-09-07T11:48:17Z"],["dc.date.issued","2008"],["dc.description.abstract","The translation initiation efficiency of a given mRNA is determined by its translation initiation region (TIR). mRNAs are selected into 30S initiation complexes according to the strengths of the secondary structure of the TIR, the pairing of the Shine-Dalgarno sequence with 16S rRNA, and the interaction between initiator tRNA and the start codon. Here, we show that the conversion of the 30S initiation complex into the translating 70S ribosome constitutes another important mRNA control checkpoint. Kinetic analysis reveals that 50S subunit joining and dissociation of IF3 are strongly influenced by the nature of the codon used for initiation and the structural elements of the TIR. Coupling between the TIR and the rate of 70S initiation complex formation involves IF3- and IF1-induced rearrangements of the 30S subunit, providing a mechanism by which the ribosome senses the TIR and determines the efficiency of translational initiation of a particular mRNA."],["dc.identifier.doi","10.1016/j.molcel.2008.04.014"],["dc.identifier.gro","3143278"],["dc.identifier.isi","000256984300006"],["dc.identifier.pmid","18570874"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/774"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1097-2765"],["dc.title","Kinetic checkpoint at a late step in translation initiation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","148"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Analytical Biochemistry"],["dc.bibliographiccitation.lastpage","150"],["dc.bibliographiccitation.volume","356"],["dc.contributor.author","Kothe, Ute"],["dc.contributor.author","Paleskava, Alena"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Rodnina, Marina"],["dc.date.accessioned","2017-09-07T11:52:31Z"],["dc.date.available","2017-09-07T11:52:31Z"],["dc.date.issued","2006"],["dc.identifier.doi","10.1016/j.ab.2006.04.038"],["dc.identifier.gro","3143626"],["dc.identifier.isi","000240170700020"],["dc.identifier.pmid","16750812"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1161"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Academic Press Inc Elsevier Science"],["dc.relation.issn","0003-2697"],["dc.title","Single-step purification of specific tRNAs by hydrophobic tagging"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","letter_note"],["dspace.entity.type","Publication"]]