Johansson lab

The research in Magnus Johansson’s lab is aimed at understanding molecular details and dynamics of protein synthesis in its context. To achieve this we are developing new fluorescence based tools to study protein synthesis on the single-molecule level inside living E. coli cells.

Popular Science Presentation

All living cells are mainly built, organized and controlled by proteins. Proteins make up muscle fibers, hairs, and skin; work as receptors on cell walls transmitting external signals to the cell interior; transport molecules from one part of the cell or body to another; and, perhaps the most interesting feature, as enzymes catalyze and control almost all chemical reactions taking place inside the living cell. The synthesis of proteins by the huge macromolecular complexes called ribosomes, according to the genetic information stored in DNA, is thus one of the most fundamental processes in all life forms. This is also reflected in the considerable fraction of all known antibiotic drugs targeting the bacterial protein synthesis machinery.

From decades of experimental work a detailed picture have been painted of how ribosomes efficiently and accurately catalyze the assembly of amino acids into proteins according to the genetic code. However, we have very limited knowledge about the regulation and dynamics of protein synthesis, in particular inside living cells, one major problem being the vast number of ribosomes in the cell pursuing different tasks at any given moment. The sheer complexity of the protein synthesis system (do we know all the players yet?), and its interplay with other processes, make it very hard to connect the molecular details of protein synthesis with cell physiology and population biology, i.e. with the level at which selection pressure applies. In our research we try to connect all these dots, in space as well as time, to get a coherent picture of one of the most fundamental processes of life. We are studying components of the protein synthesis machinery, one by one, performing their daily work inside the living cell.

“Watch PhD student Filip Ilievski’s ”3 Minute Thesis Competition” presentation regarding his project on antibiotics”

Research projects

Fluorescence based single-molecule studies of bacterial protein synthesis, in vitro and in vivo

The main focus of our research is to study protein synthesis dynamics at high spatial and temporal resolution inside living cells, with the aim of connecting molecular interactions with cell physiology and population biology.

Ribosome catalyzed protein synthesis is one of the most fundamental processes in all life forms. From decades of research, the combination of traditional biochemistry; structural approaches including NMR, cryo-EM, x-ray crystallography; and more recently single-molecule fluorescence based in vitro techniques probing structure and dynamics at the same time, have led to a very detailed picture of the molecular mechanisms of ribosome catalyzed protein synthesis. However, we have very sparse information about the dynamics of protein synthesis, in particular inside living cells, one major problem being the vast number of ribosomes in the cell pursuing different tasks at any given moment. The sheer complexity of the translational system (do we know all the players yet?), and its interplay with other processes, make it very hard to connect the molecular details of protein synthesis with cell physiology and population biology. Our research aims at connecting all these dots, in space and time, to get a coherent picture of one of the most fundamental processes of life. This is done by studying key components of the protein machinery, one by one, performing their daily work inside the living cell.

In vivo experiments are complimented by traditional biochemistry as well as in vitro single molecule fluorescence microscopy methods.

Methods

Single-molecule fluorescence microscopy, single particle tracking, super-resolution microscopy, Total Internal Reflection Fluorescence (TIRF) microscopy, ensemble biochemical methods etc.

Funding

  • European Research Counsil
  • Vetenskåpsrådet
  • Werner-Gren Stiftelserna
  • Carl Tryggers Stiftelse för Vetenskaplig Forskning

Open positions

We currently have no open positions in the laboratory. However, for highly motivated candidates we are always interested in helping out with applications for e.g. postdoc fellowships. If you are interested, please send your CV to Magnus Johansson (m.johansson@icm.uu.se), and take a look at some of the possible funding sources below:

• https://www.embo.org/funding-awards/fellowships/postdoctoral-fellowships
• https://ec.europa.eu/research/mariecurieactions/actions/individual-fellowships_en
• https://www.swgc.org/postdoktorsstipendier-sverige.aspx
• https://carltryggersstiftelse.se/ansokningar/stipendier/
• https://www.hfsp.org/funding/hfsp-funding/postdoctoral-fellowships

Group members

Research leader: Magnus Johansson

Publications

Preprints

Volkov IL, Khaji Z, Johansson M, Tenje M (2024) A microfluidic platform for in situ studies of bacteria electroporation. bioRxiv (link)

Hävermark T, Metelev M, Lundin E, Volkov IL, Johansson M (2024) Dynamic binding of the bacterial chaperone Trigger factor to translating ribosomes. bioRxiv (link)

Publications

Amselem E, Broadwater B, Hävermark T, Johansson M, Elf J (2023) Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization. Nat Commun (link)

Volkov IL, Lundin E, Kipper K, Metelev M, Zikrin S, Johansson M (2022) Spatiotemporal kinetics of the SRP pathway in live E. coli cells. Proc Natl Acad Sci U S A (link)

Tora Hävermark, Mikhail Metelev, Erik Lundin, Ivan L. Volkov, Magnus Johansson (2024) Dynamic binding of the bacterial chaperone Trigger factor to translating ribosomes. bioRxiv (link)

Amselem E, Broadwater B, Hävermark T, Johansson M, Elf J (2023) Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization. Nat Commun (link)

Volkov IL, Lundin E, Kipper K, Metelev M, Zikrin S, Johansson M (2022) Spatiotemporal kinetics of the SRP pathway in live E. coli cells. Proc Natl Acad Sci U S A (link)

Metelev M, Lundin E, Volkov IL, Gynnå AH, Elf J, Johansson M (2022) Direct measurements of mRNA translation kinetics in living cells. Nat Commun (link)

Seefeldt AC, Aguirre Rivera J, Johansson M (2021) Direct measurements of erythromycin’s effect on protein synthesis kinetics in living bacterial cells. J Mol Biol, 443 (link)

Aguirre Rivera J, Larsson J, Volkov IL, Seefeldt AC, Sanyal S, Johansson M (2021) Real-time measurements of aminoglycoside effects on protein synthesis in live cells. Proc Natl Acad Sci U S A (link)

Marklund E, van Oosten B, Mao G, Amselem E, Kipper K, Sabantsev A, Emmerich A, Globisch D, Zheng X, Lehmann LC, Berg O, Johansson M, Elf J, Deindl S (2020) DNA surface exploration and operator bypassing during target search. Nature, 583: 858-861 (link)

Volkov IL, Seefeldt AC, Johansson M (2019) Tracking of single tRNAs for translation kinetics measurements in chloramphenicol treated bacteria. Methods, 162-163: 23-30 (link)

Volkov IL, Johansson M (2019) Single-molecule tracking approaches to protein synthesis kinetics in living cells. Biochemistry, 58: 7-14 (link)

Volkov IL, Lindén M, Aguirre Rivera J, Ieong KW, Metelev M, Elf J, Johansson M (2018) tRNA tracking for direct measurements of protein synthesis kinetics in live cells. Nat Chem Biol 14: 618-626 (link)

Nilsson OB, Hedman R, Marino J, Wickles S, Bischoff L, Johansson M, Müller-Lucks A, Trovato F, Puglisi JD, O'Brien EP, Beckmann R, von Heijne G (2015) Cotranslational protein folding inside the ribosome exit tunnel. Cell reports 12: 1533-1540 (link)

Zhang J, Ieong KW, Johansson M, Ehrenberg M (2015) Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome. Proc Natl Acad Sci U S A 112: 9602-9607 (link)

Johansson M, Chen J, Tsai A, Kornberg G, Puglisi JD (2014) Sequence-dependent elongation dynamics on macrolide-bound ribosomes. Cell reports 7: 1534-1546 (link)

Tsai A, Kornberg G, Johansson M, Chen J, Puglisi JD (2014) The Dynamics of SecM-Induced Translational Stalling. Cell reports 7: 1521-1533 (link)

Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD (2014) Dynamic pathways of -1 translational frameshifting. Nature 512: 328-332 (link)

Tsai A, Uemura S, Johansson M, Puglisi EV, Marshall RA, Aitken CE, Korlach J, Ehrenberg M, Puglisi JD (2013) The impact of aminoglycosides on the dynamics of translation elongation. Cell reports 3: 497-508 (link)

Johansson M, Zhang J, Ehrenberg M (2012) Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection. Proc Natl Acad Sci U S A 109: 131-136 (link)

Johansson M., Ieong K. W., Åqvist, J., Pavlov M. Y., Ehrenberg M. (2011) Rate and accuracy of ribosomal peptidyl transfer in Ribosomes: Structure, Function and Dynamics eds. Rodnina M., Wintermeyer W., Green R. (Springer-Verlag, Wien)

Johansson M, Ieong KW, Trobro S, Strazewski P, Aqvist J, Pavlov MY, Ehrenberg M (2011) pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA. Proc Natl Acad Sci U S A 108: 79-84 (link)

Johansson M, Bouakaz E, Lovmar M, Ehrenberg M (2008) The kinetics of ribosomal peptidyl transfer revisited. Mol Cell 30: 589-598 (link)

Johansson M, Lovmar M, Ehrenberg M (2008) Rate and accuracy of bacterial protein synthesis revisited. Curr Opin Microbiol 11: 141-147 (link)

People

Magnus Johansson, Associate Professor
Office: B9:111c

Irmeli Barkefors, PhD, project coordinator

Ivan Volkov, Postdoctoral Fellow

Mikhail Metelev, Postdoctoral Fellow

Anneli Borg, Postdoctoral Fellow

Erik Lundin, PhD Student

Filip Ilievski, PhD Student

Tora Hävermark, PhD Student

Linnea Wikström, PhD Student

Alumni

Javier Aguirre Rivera, PhD student

Carolin Seefeldt, Postdoctoral Fellow

Kalle Kipper, Postdoctoral Fellow

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