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 store their genetic information in DNA, which contains the instructions for building proteins. Proteins are the molecules that carry out almost all functions of life, from metabolism and growth to communication and stress responses. Our research aims to understand, at a fundamental level, how proteins are made and handled inside living bacterial cells. We study how molecular machines called ribosomes build proteins, how newly made proteins fold into the correct shapes, how they are processed, and how they are delivered to the right place in the cell.
To do this, we use advanced single‑molecule tracking methods that allow us to follow individual molecules as they work inside living cells. By observing these processes directly and in real time, we seek to understand how complex cellular life emerges from simple molecular interactions. This fundamental knowledge also helps explain how antibiotics interfere with protein production, how bacteria can become resistant to such antibiotics, and how bacterial cells can be used more efficiently for producing useful proteins, such as therapeutic proteins used in healthcare.
Research projects
Fluorescence based single-molecule studies of bacterial protein synthesis
The main focus of our research is to study the dynamics of protein synthesis and protein biogenesis at high spatial and temporal resolution inside living bacterial cells, with the aim of connecting molecular interactions with cell physiology and population biology. We also study how these processes are perturbed by antibiotics and how bacteria respond to and evolve resistance against such inhibitors of protein synthesis.
Ribosome‑catalyzed protein synthesis is one of the most fundamental processes in all life forms, and it is also a major target for clinically important antibiotics. Decades of research combining traditional biochemistry; structural approaches including NMR, cryo‑EM, and X‑ray crystallography; and, more recently, single‑molecule fluorescence‑based in vitro techniques that probe structure and dynamics simultaneously, have led to a detailed understanding of many molecular aspects of protein biogenesis. However, we still have very limited information about the dynamic behavior of these processes inside living cells. A major challenge is the vast number of ribosomes and associated factors in the cell, simultaneously engaged in different tasks at any given moment.
Moreover, protein synthesis is tightly coupled to polypeptide folding, processing, and targeting, and these processes are embedded in a dense network of interactions with other cellular machineries. The sheer complexity of the translational system (do we know all the players yet?) and its interplay with these downstream processes make it difficult to connect molecular‑scale mechanisms to cell physiology and population‑level behavior.
Our research aims to connect these processes in space and time to obtain a coherent picture of protein biogenesis in vivo. This is achieved by studying key components of the protein synthesis, folding, and targeting pathways, one by one, as they perform their daily work inside living cells. A central aspect of our work is therefore the continuous development and application of advanced fluorescence‑based single‑molecule tracking approaches, pushing the boundaries of what can be measured in living cells in terms of spatial resolution, temporal resolution, and molecular specificity.
By linking the dynamics of protein synthesis and protein handling to antibiotic action and resistance mechanisms, our research contributes to a deeper understanding of how antibiotics function in vivo and how resistance emerges. At the same time, this knowledge has the potential to inform strategies for optimizing bacterial systems for recombinant protein production by revealing dynamic bottlenecks and regulatory constraints in the protein biogenesis pathway.
Methods
Single-molecule fluorescence microscopy, single particle tracking, super-resolution microscopy, Total Internal Reflection Fluorescence (TIRF) microscopy, ensemble biochemical methods etc.
Gruppmedlemmar
Publications
Preprints
Metelev M, Borg A, Akbar S, Larsson DSD, Seefeldt AC, Selmer M, Johansson M (2026) Ribosome collisions trigger tmRNA-mediated rescue through mRNA disengagement. bioRxiv (link)
Publikationer
Lundin L, Volkov IL, Johansson M (2026) Recovering membrane interaction kinetics of single molecules from 3D tracking data. Biophys J (link)
Ilievski F, Wikström L, Borg A, Volkov IL, Brandis G, Johansson M (2025) Optimization of the genetic code expansion technology for intracellular labelling and single-molecule tracking of proteins in genomically re-coded E. coli. RSC Chemical Biology (link)
Metelev M, Johansson M (2025) A complex between IF2 and NusA suggests early coupling of transcription-translation. Nat Commun (link)
Hävermark T, Metelev M, Lundin E, Volkov IL, Johansson M (2024) Dynamic binding of the bacterial chaperone Trigger factor to translating ribosomes in Escherichia coli. Proc Natl Acad Sci U S A (link)
Volkov IL, Khaji Z, Johansson M, Tenje M (2024) A microfluidic platform for in situ studies of bacteria electroporation. Adv Mater Technol (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)
Alumni
Javier Aguirre Rivera, PhD student
Carolin Seefeldt, Postdoctoral Fellow
Kalle Kipper, Postdoctoral Fellow
Anneli Borg, Postdoctoral Fellow
Erik Lundin, PhD Student
Filip Ilievski, PhD Student
Tora Hävermark, PhD Student