Sharma, Heena

[["dc.bibliographiccitation.firstpage","1197"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","RNA Biology"],["dc.bibliographiccitation.lastpage","1203"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Belardinelli, Riccardo"],["dc.contributor.author","Sharma, Heena"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina"],["dc.date.accessioned","2017-09-07T11:54:04Z"],["dc.date.available","2017-09-07T11:54:04Z"],["dc.date.issued","2016"],["dc.description.abstract","In each round of translation elongation, tRNAs and mRNA move within the ribosome by one codon at a time. tRNA–mRNA translocation is promoted by elongation factor G (EF-G) at the cost of GTP hydrolysis. The key questions for understanding translocation are how and when the tRNAs move and how EF-G coordinates motions of the ribosomal subunits with tRNA movement. Here we present 2 recent papers which describe the choreography of movements over the whole trajectory of translocation. We present the view that EF-G accelerates translocation by promoting the steps that lead to GTPase-dependent ribosome unlocking. EF-G facilitates the formation of the rotated state of the ribosome and uncouples the backward motions of the ribosomal subunits, forming an open conformation in which the tRNAs can rapidly move. Ribosome dynamics are important not only in translocation, but also in recoding events, such as frameshifting and bypassing, and mediate sensitivity to antibiotics."],["dc.identifier.doi","10.1080/15476286.2016.1240140"],["dc.identifier.gro","3145096"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2795"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.relation.issn","1547-6286"],["dc.subject","EF-G; mRNA; molecular machines; protein synthesis; ribosome; tRNA; translation; translation elongation; translocation"],["dc.title","Translocation as continuous movement through the ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","981"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","RNA"],["dc.bibliographiccitation.lastpage","990"],["dc.bibliographiccitation.volume","27"],["dc.contributor.author","Belardinelli, Riccardo"],["dc.contributor.author","Sharma, Heena"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2022-03-01T11:44:06Z"],["dc.date.available","2022-03-01T11:44:06Z"],["dc.date.issued","2021"],["dc.description.abstract","Many antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA movement), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, their kinetic effect on the EF-G-induced transition to the rotated/swiveled state of the SSU is moderate. The antibiotics mostly inhibit backward movements of the SSU body and/or the head domains. Vio, Spc, and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB, and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action."],["dc.description.abstract","Many antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA movement), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, their kinetic effect on the EF-G-induced transition to the rotated/swiveled state of the SSU is moderate. The antibiotics mostly inhibit backward movements of the SSU body and/or the head domains. Vio, Spc, and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB, and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action."],["dc.identifier.doi","10.1261/rna.078758.121"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/102926"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1469-9001"],["dc.relation.issn","1355-8382"],["dc.title","Perturbation of ribosomal subunit dynamics by inhibitors of tRNA translocation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","342"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Nature Structural & Molecular Biology"],["dc.bibliographiccitation.lastpage","348"],["dc.bibliographiccitation.volume","23"],["dc.contributor.author","Belardinelli, Riccardo"],["dc.contributor.author","Sharma, Heena"],["dc.contributor.author","Caliskan, Neva"],["dc.contributor.author","Cunha, Carlos E. da"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2017-09-07T11:54:33Z"],["dc.date.available","2017-09-07T11:54:33Z"],["dc.date.issued","2016"],["dc.description.abstract","During translation elongation, ribosome translocation along an mRNA entails rotations of the ribosomal subunits, swiveling motions of the small subunit (SSU) head and stepwise movements of the tRNAs together with the mRNA. Here, we reconstructed the choreography of the collective motions of the Escherichia coli ribosome during translocation promoted by elongation factor EF-G, by recording the fluorescence signatures of nine different reporters placed on both ribosomal subunits, tRNA and mRNA. We captured an early forward swiveling of the SSU head taking place while the SSU body rotates in the opposite, clockwise direction. Backward swiveling of the SSU head starts upon tRNA translocation and continues until the post-translocation state is reached. This work places structures of translocation intermediates along a time axis and unravels principles of the motions of macromolecular machines."],["dc.identifier.doi","10.1038/nsmb.3193"],["dc.identifier.gro","3141703"],["dc.identifier.isi","000373658300012"],["dc.identifier.pmid","26999556"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/136"],["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","1545-9985"],["dc.relation.issn","1545-9993"],["dc.title","Choreography of molecular movements during ribosome progression along mRNA"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","eLife"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Adio, Sarah"],["dc.contributor.author","Sharma, Heena"],["dc.contributor.author","Senyushkina, Tamara"],["dc.contributor.author","Karki, Prajwal"],["dc.contributor.author","Maracci, Cristina"],["dc.contributor.author","Wohlgemuth, Ingo"],["dc.contributor.author","Holtkamp, Wolf"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2019-07-25T11:30:31Z"],["dc.date.available","2019-07-25T11:30:31Z"],["dc.date.issued","2018"],["dc.description.abstract","Release factors RF1 and RF2 promote hydrolysis of peptidyl-tRNA during translation termination. The GTPase RF3 promotes recycling of RF1 and RF2. Using single molecule FRET and biochemical assays, we show that ribosome termination complexes that carry two factors, RF1-RF3 or RF2-RF3, are dynamic and fluctuate between non-rotated and rotated states, whereas each factor alone has its distinct signature on ribosome dynamics and conformation. Dissociation of RF1 depends on peptide release and the presence of RF3, whereas RF2 can dissociate spontaneously. RF3 binds in the GTP-bound state and can rapidly dissociate without GTP hydrolysis from termination complex carrying RF1. In the absence of RF1, RF3 is stalled on ribosomes if GTP hydrolysis is blocked. Our data suggest how the assembly of the ribosome-RF1-RF3-GTP complex, peptide release, and ribosome fluctuations promote termination of protein synthesis and recycling of the release factors."],["dc.identifier.doi","10.7554/eLife.34252"],["dc.identifier.pmid","29889659"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/62052"],["dc.language.iso","en"],["dc.relation.eissn","2050-084X"],["dc.relation.issn","2050-084X"],["dc.title","Dynamics of ribosomes and release factors during translation termination in E. coli"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2187"],["dc.bibliographiccitation.issue","8"],["dc.bibliographiccitation.journal","Cell Reports"],["dc.bibliographiccitation.lastpage","2196"],["dc.bibliographiccitation.volume","16"],["dc.contributor.author","Sharma, Heena"],["dc.contributor.author","Adio, Sarah"],["dc.contributor.author","Senyushkina, Tamara"],["dc.contributor.author","Belardinelli, Riccardo"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2017-09-07T11:44:43Z"],["dc.date.available","2017-09-07T11:44:43Z"],["dc.date.issued","2016"],["dc.description.abstract","Ribosome dynamics play an important role in translation. The rotation of the ribosomal subunits relative to one another is essential for tRNA-mRNA translocation. An important unresolved question is whether subunit rotation limits the rate of translocation. Here, we monitor subunit rotation relative to peptide bond formation and translocation using ensemble kinetics and single-molecule FRET. We observe that spontaneous forward subunit rotation occurs at a rate of 40 s(-1), independent of the rate of preceding peptide bond formation. Elongation factor G (EF-G) accelerates forward subunit rotation to 200 s(-1). tRNA-mRNA movement is much slower (10-40 s(-1)), suggesting that forward subunit rotation does not limit the rate of translocation. The transition back to the non-rotated state of the ribosome kinetically coincides with tRNA-mRNA movement. Thus, largescale movements of the ribosome are intrinsically rapid and gated by its ligands such as EF-G and tRNA."],["dc.identifier.doi","10.1016/j.celrep.2016.07.051"],["dc.identifier.gro","3141633"],["dc.identifier.isi","000382310100015"],["dc.identifier.pmid","27524615"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/3456"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Deutsche Forschungsgemeinschaft [Sonderforschungsbereich 860]"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","2211-1247"],["dc.title","Kinetics of Spontaneous and EF-G-Accelerated Rotation of Ribosomal Subunits"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]