Michel, Benoît Y., Krishnakumar, Kollappillil S., Johansson, Magnus, Ehrenberg, Måns, Strazewski, Peter
Aminoacyl ribonucleoside analogues that are capable of binding to the acceptor site of ribosomes and taking over the nascent peptide bear, if properly designed, thepotential of antibiotic and...
Andreev, Dmitri, Hauryliuk, Vasili, Terenin, Ilya, Dmitriev, Sergey, Ehrenberg, Måns, Shatsky, Ivan
RelE/RelB is a well-characterized toxin–anti-toxin pair involved in nutritional stress responses in Bacteria and Archae. RelE lacks any eukaryote homolog, but we demonstrate here that it...
Structure probing of tmRNA in distinct stages of trans-translation (2007)
Ivanova, Natalia, Lindell, Magnus, Pavlov, Michael, Holmberg Schiavone, Lovisa, Wagner, E. Gerhart H., Ehrenberg, Måns
Ribosomes stalled on problematic mRNAs in bacterial cells can be rescued by transfer-messenger RNA (tmRNA), its helper protein (small protein B, SmpB), and elongation factor Tu (EF-Tu) through a...
Zavialov, Andrey V, Hauryliuk, Vasili V, Ehrenberg, Måns
Abstract Background During the translation of mRNA into polypeptide, elongation factor G (EF-G) catalyzes the translocation of peptidyl-tRNA from the A site to the P site of the ribosome. According...
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation? (2005)
Ribosome-mediated transcriptional attenuation mechanisms are commonly used to control amino acid biosynthetic operons in bacteria. The mRNA leader of such an operon contains an open reading frame...
Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA (2005)
Ivanova, Natalia, Pavlov, Michael Y., Bouakaz, Elli, Ehrenberg, Måns, Schiavone, Lovisa Holmberg
In trans-translation transfer messenger RNA (tmRNA) and small protein B (SmpB) rescue ribosomes stalled on truncated or in other ways problematic mRNAs. SmpB promotes the binding of tmRNA to the...
Systems Biology Is Taking Off (2003)
Ehrenberg, Måns, Elf, Johan, Aurell, Erik, Sandberg, Rickard, Tegnér, Jesper
Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation (2003)
Biochemical networks in single cells can display large fluctuations in molecule numbers, making mesoscopic approaches necessary for correct system descriptions. We present a general method that...
The accuracy of codon recognition by polypeptide release factors
Freistroffer, David V., Kwiatkowski, Marek, Buckingham, Richard H., Ehrenberg, Måns
The precision with which individual termination codons in mRNA are recognized by protein release factors (RFs) has been measured and compared with the decoding of sense codons by tRNA. An Escherichia...
Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation
Paulsson, Johan, Berg, Otto G., Ehrenberg, Måns
Many regulatory molecules are present in low copy numbers per cell so that significant random fluctuations emerge spontaneously. Because cell viability depends on precise regulation of key events,...
Randall, Linda L., Topping, Traci B., Hardy, Simon J. S., Pavlov, Michael Y., Freistroffer, David V., Ehrenberg, Måns
The interaction of the chaperone SecB with ribosome-bound polypeptides that are in the process of elongation has been studied using an in vitro protein synthesis system. The binding is characterized...
Heurgué-Hamard, Valérie, Champ, Stéphanie, Engström, Åke, Ehrenberg, Måns, Buckingham, Richard H.
Class 1 peptide release factors (RFs) in Escherichia coli are N5-methylated on the glutamine residue of the universally conserved GGQ motif. One other protein alone has been shown to contain...
NEW EMBO MEMBER’S REVIEW: Termination of translation: interplay of mRNA, rRNAs and release factors?
Kisselev, Lev, Ehrenberg, Måns, Frolova, Ludmila
Termination of translation in eukaryotes has focused recently on functional anatomy of polypeptide chain release factor, eRF1, by using a variety of different approaches. The tight correlation...
Origins of minigene-dependent growth inhibition in bacterial cells
Heurgué-Hamard, Valérie, Dinçbas, Vildan, Buckingham, Richard H., Ehrenberg, Måns
The expression of very short open reading frames in Escherichia coli can lead to the inhibition of translation and an arrest in cell growth. Inhibition occurs because peptidyl-tRNA hydrolase fails to...
The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis
Antoun, Ayman, Pavlov, Michael Y., Andersson, Kerstin, Tenson, Tanel, Ehrenberg, Måns
The role of IF2 from Escherichia coli was studied in vitro using a system for protein synthesis with purified components. Stopped flow experiments with light scattering show that IF2 in complex with...
Dinçbas-Renqvist, Vildan, Engström, Åke, Mora, Liliana, Heurgué-Hamard, Valérie, Buckingham, Richard, Ehrenberg, Måns
A post-translational modification affecting the translation termination rate was identified in the universally conserved GGQ sequence of release factor 2 (RF2) from Escherichia coli, which is thought...
Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering
Antoun, Ayman, Pavlov, Michael Y., Tenson, Tanel, Ehrenberg, Måns
Light scattering and standard stopped-flow techniques were used to monitor rapid association of ribosomal subunits during initiation of eubacterial protein synthesis. The effects of the initiation...
Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation
Biochemical networks in single cells can display large fluctuations in molecule numbers, making mesoscopic approaches necessary for correct system descriptions. We present a general method that...
Catalytic effects of elongation factor Ts on polypeptide synthesis
Ruusala, Tarmo, Ehrenberg, Måns, Kurland, Charles G.
The kinetic parameters which characterize the interaction between elongation factor Tu (EF-Tu) and elongation factor Ts (EF-Ts) have been determined in a poly(uridylic acid)-primed translation...
Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA
Ivanova, Natalia, Pavlov, Michael Y., Bouakaz, Elli, Ehrenberg, Måns, Schiavone, Lovisa Holmberg
In trans-translation transfer messenger RNA (tmRNA) and small protein B (SmpB) rescue ribosomes stalled on truncated or in other ways problematic mRNAs. SmpB promotes the binding of tmRNA to the...
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?
Ribosome-mediated transcriptional attenuation mechanisms are commonly used to control amino acid biosynthetic operons in bacteria. The mRNA leader of such an operon contains an open reading frame...
Ribosome bypassing at serine codons as a test of the model of selective transfer RNA charging
Lindsley, Dale, Bonthuis, Paul, Gallant, Jonathan, Tofoleanu, Teodora, Elf, Johan, Ehrenberg, Måns
Recently, a model of the flux of amino acids through transfer RNAs (tRNAs) and into protein has been developed. The model predicts that the charging level of different isoacceptors carrying the same...
Selective charging of tRNA isoacceptors induced by amino-acid starvation
Dittmar, Kimberly A, Sørensen, Michael A, Elf, Johan, Ehrenberg, Måns, Pan, Tao
Aminoacylated (charged) transfer RNA isoacceptors read different messenger RNA codons for the same amino acid. The concentration of an isoacceptor and its charged fraction are principal determinants...
Near-Critical Phenomena in Intracellular Metabolite Pools
Elf, Johan, Paulsson, Johan, Berg, Otto G., Ehrenberg, Måns
The supply and consumption of metabolites in living cells are catalyzed by enzymes. Here we consider two of the simplest schemes where one substrate is eliminated through Michaelis-Menten kinetics,...
Near-Critical Behavior of Aminoacyl-tRNA Pools in E. coli at Rate-Limiting Supply of Amino Acids
The rates of consumption of different amino acids in protein synthesis are in general stoichiometrically coupled with coefficients determined by codon usage frequencies on translating ribosomes. We...
The Cryo-EM Structure of a Translation Initiation Complex from Escherichia coli.
Allen, Gregory S., Zavialov, Andrey, Gursky, Richard, Ehrenberg, Måns, Frank, Joachim
The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex...
The accuracy of codon recognition by polypeptide release factors
Freistroffer, David V., Kwiatkowski, Marek, Buckingham, Richard H., Ehrenberg, Måns
The precision with which individual termination codons in mRNA are recognized by protein release factors (RFs) has been measured and compared with the decoding of sense codons by tRNA. An Escherichia...
Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation
Paulsson, Johan, Berg, Otto G., Ehrenberg, Måns
Many regulatory molecules are present in low copy numbers per cell so that significant random fluctuations emerge spontaneously. Because cell viability depends on precise regulation of key events,...
Randall, Linda L., Topping, Traci B., Hardy, Simon J. S., Pavlov, Michael Y., Freistroffer, David V., Ehrenberg, Måns
The interaction of the chaperone SecB with ribosome-bound polypeptides that are in the process of elongation has been studied using an in vitro protein synthesis system. The binding is characterized...
Heurgué-Hamard, Valérie, Champ, Stéphanie, Engström, Åke, Ehrenberg, Måns, Buckingham, Richard H.
Class 1 peptide release factors (RFs) in Escherichia coli are N5-methylated on the glutamine residue of the universally conserved GGQ motif. One other protein alone has been shown to contain...
NEW EMBO MEMBER’S REVIEW: Termination of translation: interplay of mRNA, rRNAs and release factors?
Kisselev, Lev, Ehrenberg, Måns, Frolova, Ludmila
Termination of translation in eukaryotes has focused recently on functional anatomy of polypeptide chain release factor, eRF1, by using a variety of different approaches. The tight correlation...
Origins of minigene-dependent growth inhibition in bacterial cells
Heurgué-Hamard, Valérie, Dinçbas, Vildan, Buckingham, Richard H., Ehrenberg, Måns
The expression of very short open reading frames in Escherichia coli can lead to the inhibition of translation and an arrest in cell growth. Inhibition occurs because peptidyl-tRNA hydrolase fails to...
The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis
Antoun, Ayman, Pavlov, Michael Y., Andersson, Kerstin, Tenson, Tanel, Ehrenberg, Måns
The role of IF2 from Escherichia coli was studied in vitro using a system for protein synthesis with purified components. Stopped flow experiments with light scattering show that IF2 in complex with...
Dinçbas-Renqvist, Vildan, Engström, Åke, Mora, Liliana, Heurgué-Hamard, Valérie, Buckingham, Richard, Ehrenberg, Måns
A post-translational modification affecting the translation termination rate was identified in the universally conserved GGQ sequence of release factor 2 (RF2) from Escherichia coli, which is thought...
Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering
Antoun, Ayman, Pavlov, Michael Y., Tenson, Tanel, Ehrenberg, Måns
Light scattering and standard stopped-flow techniques were used to monitor rapid association of ribosomal subunits during initiation of eubacterial protein synthesis. The effects of the initiation...
Fast Evaluation of Fluctuations in Biochemical Networks With the Linear Noise Approximation
Biochemical networks in single cells can display large fluctuations in molecule numbers, making mesoscopic approaches necessary for correct system descriptions. We present a general method that...
Catalytic effects of elongation factor Ts on polypeptide synthesis
Ruusala, Tarmo, Ehrenberg, Måns, Kurland, Charles G.
The kinetic parameters which characterize the interaction between elongation factor Tu (EF-Tu) and elongation factor Ts (EF-Ts) have been determined in a poly(uridylic acid)-primed translation...
Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA
Ivanova, Natalia, Pavlov, Michael Y., Bouakaz, Elli, Ehrenberg, Måns, Schiavone, Lovisa Holmberg
In trans-translation transfer messenger RNA (tmRNA) and small protein B (SmpB) rescue ribosomes stalled on truncated or in other ways problematic mRNAs. SmpB promotes the binding of tmRNA to the...
What Makes Ribosome-Mediated Transcriptional Attenuation Sensitive to Amino Acid Limitation?
Ribosome-mediated transcriptional attenuation mechanisms are commonly used to control amino acid biosynthetic operons in bacteria. The mRNA leader of such an operon contains an open reading frame...
Ribosome bypassing at serine codons as a test of the model of selective transfer RNA charging
Lindsley, Dale, Bonthuis, Paul, Gallant, Jonathan, Tofoleanu, Teodora, Elf, Johan, Ehrenberg, Måns
Recently, a model of the flux of amino acids through transfer RNAs (tRNAs) and into protein has been developed. The model predicts that the charging level of different isoacceptors carrying the same...
Selective charging of tRNA isoacceptors induced by amino-acid starvation
Dittmar, Kimberly A, Sørensen, Michael A, Elf, Johan, Ehrenberg, Måns, Pan, Tao
Aminoacylated (charged) transfer RNA isoacceptors read different messenger RNA codons for the same amino acid. The concentration of an isoacceptor and its charged fraction are principal determinants...
Near-Critical Phenomena in Intracellular Metabolite Pools
Elf, Johan, Paulsson, Johan, Berg, Otto G., Ehrenberg, Måns
The supply and consumption of metabolites in living cells are catalyzed by enzymes. Here we consider two of the simplest schemes where one substrate is eliminated through Michaelis-Menten kinetics,...
Near-Critical Behavior of Aminoacyl-tRNA Pools in E. coli at Rate-Limiting Supply of Amino Acids
The rates of consumption of different amino acids in protein synthesis are in general stoichiometrically coupled with coefficients determined by codon usage frequencies on translating ribosomes. We...
How initiation factors tune the rate of initiation of protein synthesis in bacteria
Antoun, Ayman, Pavlov, Michael Y, Lovmar, Martin, Ehrenberg, Måns
The kinetics of initiator transfer RNA (tRNA) interaction with the messenger RNA (mRNA)-programmed 30S subunit and the rate of 50S subunit docking to the 30S preinitiation complex were measured for...
Structure probing of tmRNA in distinct stages of trans-translation
Ivanova, Natalia, Lindell, Magnus, Pavlov, Michael, Holmberg Schiavone, Lovisa, Wagner, E. Gerhart H., Ehrenberg, Måns
Ribosomes stalled on problematic mRNAs in bacterial cells can be rescued by transfer-messenger RNA (tmRNA), its helper protein (small protein B, SmpB), and elongation factor Tu (EF-Tu) through a...
Ullers, Ronald S., Houben, Edith N.G., Raine, Amanda, Ehrenberg, Måns, Brunner, Joseph, ...
As newly synthesized polypeptides emerge from the ribosome, they interact with chaperones and targeting factors that assist in folding and targeting to the proper location in the cell. In Escherichia...
The bacterial toxin RelE induces specific mRNA cleavage in the A site of the eukaryote ribosome
Andreev, Dmitri, Hauryliuk, Vasili, Terenin, Ilya, Dmitriev, Sergey, Ehrenberg, Måns, Shatsky, Ivan
RelE/RelB is a well-characterized toxin–anti-toxin pair involved in nutritional stress responses in Bacteria and Archae. RelE lacks any eukaryote homolog, but we demonstrate here that it...
The pretranslocation ribosome is targeted by GTP-bound EF-G in partially activated form
Hauryliuk, Vasili, Mitkevich, Vladimir A., Eliseeva, Natalia A., Petrushanko, Irina Yu., Ehrenberg, Måns, Makarov, Alexander A.
Translocation of the tRNA·mRNA complex through the bacterial ribosome is driven by the multidomain guanosine triphosphatase elongation factor G (EF-G). We have used isothermal titration calorimetry...
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM
Li, Wen, Agirrezabala, Xabier, Lei, Jianlin, Bouakaz, Lamine, Brunelle, Julie L, Ortiz-Meoz, Rodrigo F, ...
The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes...
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis
Villa, Elizabeth, Sengupta, Jayati, Trabuco, Leonardo G., LeBarron, Jamie, Baxter, William T., Shaikh, Tanvir R., ...
In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of...
Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting
Pavlov, Michael Y, Antoun, Ayman, Lovmar, Martin, Ehrenberg, Måns
We demonstrate that ribosomes containing a messenger RNA (mRNA) with a strong Shine–Dalgarno sequence are rapidly split into subunits by initiation factors 1 (IF1) and 3 (IF3), but slowly split by...
Slow peptide bond formation by proline and other N-alkylamino acids in translation
Pavlov, Michael Y., Watts, Richard E., Tan, Zhongping, Cornish, Virginia W., Ehrenberg, Måns, Forster, Anthony C.
Proteins are made from 19 aa and, curiously, one N-alkylamino acid (“imino acid”), proline (Pro). Pro is thought to be incorporated by the translation apparatus at the same rate as the 19 aa,...
Cofactor Dependent Conformational Switching of GTPases
Hauryliuk, Vasili, Hansson, Sebastian, Ehrenberg, Måns
This theoretical work covers structural and biochemical aspects of nucleotide binding and GDP/GTP exchange of GTP hydrolases belonging to the family of small GTPases. Current models of GDP/GTP...
Drug efflux pump deficiency and drug target resistance masking in growing bacteria
Fange, David, Nilsson, Karin, Tenson, Tanel, Ehrenberg, Måns
Recent experiments have shown that drug efflux pump deficiency not only increases the susceptibility of pathogens to antibiotics, but also seems to “mask” the effects of mutations, that decrease...