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Ehrenberg, Måns
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Publications (10 of 79) Show all publications
Choi, J., Indrisiunaite, G., DeMirci, H., Leong, K.-W., Wang, J., Petrov, A., . . . Puglisi, J. D. (2018). 2 '-O-methylation in mRNA disrupts tRNA decoding during translation elongation. Nature Structural & Molecular Biology, 25(3), 208-216
Open this publication in new window or tab >>2 '-O-methylation in mRNA disrupts tRNA decoding during translation elongation
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2018 (English)In: Nature Structural & Molecular Biology, ISSN 1545-9993, E-ISSN 1545-9985, Vol. 25, no 3, p. 208-216Article in journal (Refereed) Published
Abstract [en]

Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2 '-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2 '-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2 '-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-350295 (URN)10.1038/s41594-018-0030-z (DOI)000426704000006 ()29459784 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2018-05-09 Created: 2018-05-09 Last updated: 2018-05-09Bibliographically approved
Zhang, J., Pavlov, M. & Ehrenberg, M. (2018). Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions. Nucleic Acids Research, 46(3), 1362-1374
Open this publication in new window or tab >>Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions
2018 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 46, no 3, p. 1362-1374Article in journal (Refereed) Published
Abstract [en]

We studied the effects of aminoglycosides and changing Mg2+ ion concentration on the accuracy of initial codon selection by aminoacyl-tRNA in ternary complex with elongation factor Tu and GTP (T-3) on mRNA programmed ribosomes. Aminoglycosides decrease the accuracy by changing the equilibrium constants of 'monitoring bases' A1492, A1493 and G530 in 16S rRNA in favor of their 'activated' state by large, aminoglycoside-specific factors, which are the same for cognate and near-cognate codons. Increasing Mg2+ concentration decreases the accuracy by slowing dissociation of T-3 from its initial codon-and aminoglycoside-independent binding state on the ribosome. The distinct accuracy-corrupting mechanisms for aminoglycosides and Mg2+ ions prompted us to re-interpret previous biochemical experiments and functional implications of existing high resolution ribosome structures. We estimate the upper thermodynamic limit to the accuracy, the 'intrinsic selectivity' of the ribosome. We conclude that aminoglycosides do not alter the intrinsic selectivity but reduce the fraction of it that is expressed as the accuracy of initial selection. We suggest that induced fit increases the accuracy and speed of codon reading at unaltered intrinsic selectivity of the ribosome.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-349357 (URN)10.1093/nar/gkx1256 (DOI)000425294400033 ()29267976 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2018-05-02 Created: 2018-05-02 Last updated: 2018-05-02Bibliographically approved
Fislage, M., Zhang, J., Brown, Z. P., Mandava, C. S., Sanyal, S., Ehrenberg, M. & Frank, J. (2018). Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-Tu(H84A). Nucleic Acids Research, 46(11), 5861-5874
Open this publication in new window or tab >>Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-Tu(H84A)
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2018 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 46, no 11, p. 5861-5874Article in journal (Refereed) Published
Abstract [en]

The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of themonitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-361119 (URN)10.1093/nar/gky346 (DOI)000438362400042 ()29733411 (PubMedID)
Funder
Swedish Research Council, 2013-8778Swedish Research Council, 2014-4423Swedish Research Council, 2016-06264Swedish Research Council, 2017-00230Knut and Alice Wallenberg Foundation, KAW 2011.0081NIH (National Institute of Health), R01 GM29169
Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-09-20Bibliographically approved
Choi, J., Indrisiunaite, G., DeMirci, H., Ieong, K.-W., Wang, J., Petrov, A., . . . Puglisi, J. D. (2018). How 2 '-O-Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation. Paper presented at 62nd Annual Meeting of the Biophysical-Society, FEB 17-21, 2018, San Francisco, CA. Biophysical Journal, 114(3), 592A-592A
Open this publication in new window or tab >>How 2 '-O-Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation
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2018 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, no 3, p. 592A-592AArticle in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
CELL PRESS, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-357497 (URN)000430563200717 ()
Conference
62nd Annual Meeting of the Biophysical-Society, FEB 17-21, 2018, San Francisco, CA
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-08-17Bibliographically approved
Pavlov, M. & Ehrenberg, M. (2018). Substrate-Induced Formation of Ribosomal Decoding Center for Accurate and Rapid Genetic Code Translation. Annual Review of Biophysics, 525-548
Open this publication in new window or tab >>Substrate-Induced Formation of Ribosomal Decoding Center for Accurate and Rapid Genetic Code Translation
2018 (English)In: Annual Review of Biophysics, ISSN 1936-122X, E-ISSN 1936-1238, p. 525-548Article, review/survey (Refereed) Published
Abstract [en]

Accurate translation of genetic information is crucial for synthesis of functional proteins in all organisms. We use recent experimental data to discuss how induced fit affects accuracy of initial codon selection on the ribosome by aminoacyl transfer RNA in ternary complex (T-3) with elongation factor Tu (EF-Tu) and guanosine-5'-triphosphate (GTP). We define actual accuracy (A(I)(nc)) of a particular protein synthesis system as its current accuracy and the effective selectivity (d(eI)(nc)) as A(I)(nc) in the limit of zero ribosomal binding affinity for T-3. Intrinsic selectivity (D-I(nc)), defined as the upper thermodynamic limit of d(eI)(nc), is determined by the free energy difference between near-cognate and cognate T-3 in the pre-GTP hydrolysis state on the ribosome. D-I(nc) is much larger than d(eI)(nc), suggesting the possibility of a considerable increase in d(eI)(nc) and A(I)(nc) at negligible kinetic cost. Induced fit increases A(I)(nc) and d(eI)(nc) without affecting D-I(nc), and aminoglycoside antibiotics reduce A(I)(nc) and d(eI)(nc) at unaltered D-I(nc).

Keywords
induced fit, ribosome, translation accuracy, initial selection, tautomers
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-361439 (URN)10.1146/annurev-biophys-060414-034148 (DOI)000433056800024 ()29792818 (PubMedID)978-0-8243-1847-5 (ISBN)
Available from: 2018-12-10 Created: 2018-12-10 Last updated: 2018-12-10Bibliographically approved
Caban, K., Pavlov, M., Kaledhonkar, S., Fu, Z., Frank, J., Ehrenberg, M. & Gonzalez, R. L. . (2018). The Structural Basis for Initiation Factor 2 Activation during Translation Initiation. Paper presented at 62nd Annual Meeting of the Biophysical-Society, FEB 17-21, 2018, San Francisco, CA, USA. Biophysical Journal, 114(3), 593A-593A
Open this publication in new window or tab >>The Structural Basis for Initiation Factor 2 Activation during Translation Initiation
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2018 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, no 3, p. 593A-593AArticle in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
CELL PRESS, 2018
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-357498 (URN)000430563200723 ()
Conference
62nd Annual Meeting of the Biophysical-Society, FEB 17-21, 2018, San Francisco, CA, USA
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-08-17Bibliographically approved
Caban, K., Pavlov, M., Ehrenberg, M. & Gonzalez, R. L. . (2017). A conformational switch in initiation factor 2 controls the fidelity of translation initiation in bacteria. Nature Communications, 8, Article ID 1475.
Open this publication in new window or tab >>A conformational switch in initiation factor 2 controls the fidelity of translation initiation in bacteria
2017 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 1475Article in journal (Refereed) Published
Abstract [en]

Initiation factor (IF) 2 controls the fidelity of translation initiation by selectively increasing the rate of 50S ribosomal subunit joining to 30S initiation complexes (ICs) that carry an N-formyl-methionyl-tRNA (fMet-tRNA(fMet)). Previous studies suggest that rapid 50S subunit joining involves a GTP- and fMet-tRNA(fMet)-dependent "activation" of IF2, but a lack of data on the structure and conformational dynamics of 30S IC-bound IF2 has precluded a mechanistic understanding of this process. Here, using an IF2-tRNA single-molecule fluorescence resonance energy transfer signal, we directly observe the conformational switch that is associated with IF2 activation within 30S ICs that lack IF3. Based on these results, we propose a model of IF2 activation that reveals how GTP, fMet-tRNA(fMet), and specific structural elements of IF2 drive and regulate this conformational switch. Notably, we find that domain III of IF2 plays a pivotal, allosteric, role in IF2 activation, suggesting that this domain can be targeted for the development of novel antibiotics.

National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-342388 (URN)10.1038/s41467-017-01492-6 (DOI)000415124000002 ()29133802 (PubMedID)
Funder
NIH (National Institute of Health), R01 GM 084288
Available from: 2018-02-22 Created: 2018-02-22 Last updated: 2018-02-22Bibliographically approved
Pavlov, M., Liljas, A. & Ehrenberg, M. (2017). A recent intermezzo at the Ribosome Club. Philosophical Transactions of the Royal Society of London. Biological Sciences, 372(1716), Article ID 20160185.
Open this publication in new window or tab >>A recent intermezzo at the Ribosome Club
2017 (English)In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 372, no 1716, article id 20160185Article, review/survey (Refereed) Published
Abstract [en]

Two sets of ribosome structures have recently led to two different interpretations of what limits the accuracy of codon translation by transfer RNAs. In this review, inspired by this intermezzo at the Ribosome Club, we briefly discuss accuracy amplification by energy driven proofreading and its implementation in genetic code translation. We further discuss general ways by which the monitoring bases of 16S rRNA may enhance the ultimate accuracy (d-values) and how the codon translation accuracy is reduced by the actions of Mg2+ ions and the presence of error inducing aminoglycoside antibiotics. We demonstrate that complete freezing-in of cognate-like tautomeric states of ribosome-bound nucleotide bases in transfer RNA or messenger RNA is not compatible with recent experiments on initial codon selection by transfer RNA in ternary complex with elongation factor Tu and GTP. From these considerations, we suggest that the sets of 30S subunit structures from the Ramakrishnan group and 70S structures from the Yusupov/Yusupova group may, after all, reflect two sides of the same coin and how the structurally based intermezzo at the Ribosome Club may be resolved simply by taking the dynamic aspects of ribosome function into account. This article is part of the themed issue 'Perspectives on the ribosome'.

Keywords
ribosome, translation accuracy, proofreading, initial transfer RNA selection, tautomers
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-317503 (URN)10.1098/rstb.2016.0185 (DOI)000393403600008 ()
Available from: 2017-04-13 Created: 2017-04-13 Last updated: 2018-01-13
Reuveni, S., Ehrenberg, M. & Paulsson, J. (2017). Ribosomes are optimized for autocatalytic production. Nature, 547(7663), 293-297
Open this publication in new window or tab >>Ribosomes are optimized for autocatalytic production
2017 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 547, no 7663, p. 293-297Article in journal (Refereed) Published
Abstract [en]

Many fine-scale features of ribosomes have been explained in terms of function, revealing a molecular machine that is optimized for error-correction, speed and control. Here we demonstrate mathematically that many less well understood, larger-scale features of ribosomes-such as why a few ribosomal RNA molecules dominate the mass and why the ribosomal protein content is divided into 55-80 small, similarly sized segments-speed up their autocatalytic production.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-332850 (URN)10.1038/nature22998 (DOI)000405844900023 ()28726822 (PubMedID)
Funder
Swedish Research Council
Available from: 2017-11-08 Created: 2017-11-08 Last updated: 2017-11-08Bibliographically approved
Mellenius, H. & Ehrenberg, M. (2017). Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase. Nucleic Acids Research, 45(20), 11582-11593
Open this publication in new window or tab >>Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase
2017 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no 20, p. 11582-11593Article in journal (Refereed) Published
Abstract [en]

We suggest a novel two-step proofreading mechanism with two sequential rounds of proofreading selection in mRNA transcription. It is based on the previous experimental observations that the proofreading RNA polymerase cleaves off transcript fragments of at least 2 nt and that transcript elongation after a nucleotide misincorporation is anomalously slow. Taking these results into account, we extend the description of the accuracy of template guided nucleotide selection beyond previous models of RNA polymerase-dependent DNA transcription. The model derives the accuracy of initial and proofreading base selection from experimentally estimated nearest-neighbor parameters. It is also used to estimate the small accuracy enhancement of polymerase revisiting of previous positions following transcript cleavage.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-359630 (URN)10.1093/nar/gkx849 (DOI)000416164300016 ()29036494 (PubMedID)
Funder
Swedish Research Council, 2015-04682Knut and Alice Wallenberg Foundation, KAW 2009.0251
Available from: 2018-09-05 Created: 2018-09-05 Last updated: 2018-09-05Bibliographically approved
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