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Center for Models of Life
Niels Bohr Institute
University of Copenhagen
Blegdamsvej 17
2100 Copenhagen Ø

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Translation dynamics and regulation

Translation is the second step in converting the information from DNA to the world of proteins. Translation is done by ribosomes that translate about 13codons/sec along a mRNA (in procaryotes). mRNA in procaryotes `lives about 2-5min, and is translated between 1 and 40 times per message. mRNA lifetimes can be regulated by HfQ and sRNA, which by degrading mRNA on 1min tmescale opens for particularly fast changes of gene expression.


Namiko Mitarai, Anna M. C. Andersson, Sandeep Krishna, Szabolcs Semsey, and Kim Sneppen
Efficient degradation and expression prioritization with small RNAs
Phys. biol. 4 (2007)

Mette Eriksen, Kim Sneppen, Steen Pedersen, and Namiko Mitarai
Occlusion of the Ribosome Binding Site Connects the Translational Initiation Frequency, mRNA Stability and Premature Transcription Termination
Front. Microbiol. 8 (2017)

Sabine Hansen, Sandeep Krishna, Szabolcs Semsey, and Sine Lo Svenningsen
Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades
Scientific Reports 5 (2015)

Szabolcs Semsey
A Mixed Incoherent Feed-Forward Loop Allows Conditional Regulation of Response Dynamics
Plos One 9 (2014)

Ilaria Cataudella, Ala Trusina, Kim Sneppen, Kenn Gerdes, and Namiko Mitarai
Conditional cooperativity in toxin–antitoxin regulation prevents random toxin activation and promotes fast translational recovery
Nuc. Acids Res. 40 (2012)

Margit Pedersen, Søren Nissen, Namiko Mitarai, Sine Lo Svenningsen, Kim Sneppen, and Steen Pedersen
The Functional Half-Life of an mRNA Depends on the Ribosome Spacing in an Early Coding Region
J. Mol. Biol. 407 (2011)

Ala Trusina, Feroz Papa and Chao Tang
Translation Attenuation Mechanism in Unfolded Protein Response
Evolution from Cellular to Social Scales NATO Science for Peace and Security Series B: Physics and Biophysics 0 (2008)

Ala Trusina and Chao Tang
The unfolded protein response and translation attenuation: a modelling approach
Diabetes, Obesity and Metabolism 12 (2010)

Szabolcs Semsey, Sandeep Krishna, Janos Erdssy, Peter Horvath, Laszlo Orosz, Kim Sneppen and Sankar Adhya
Dominant Negative Autoregulation Limits Steady-State Repression Levels in Gene Networks
Journal of Bacteriology 191 (2009)

Szabolcs Semsey, Julie-Anna M. Benjamin, Namiko Mitarai, Sandeep Krishna, Zsolt Csiszovszki, Kim Sneppen and Eric Massé
Dynamics of the recovery from sRNA-mediated gene silencing
Cell Cycle 8 (2009)

Namiko Mitarai, Julie-Anna M. Benjamin, Sandeep Krishna, Szabolcs Semsey, Zsolt Csiszovszki, Eric Massé, and Kim Sneppen
Dynamic features of gene expression control by small regulatory RNAs
Proc. Natl. Acad. Sci. USA 106 (2009)

Namiko Mitarai, Kim Sneppen, Steen Pedersen
Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization
J. Mol. Biol. 382 (2008)

Jacob Bock Axelsen and Kim Sneppen
Quantifying the benefits of translation regulation in the unfolded protein response
Phys. Biol. 1 (2004)

Szabolcs Semsey, Anna M. C. Andersson, Sandeep Krishna, Mogens Høgh Jensen, Eric Massé, and Kim Sneppen
Genetic regulation of fluxes: Iron homeostasis of Escherichia coli
Nucleic Acids Research 34 (2006)

Yusuke Himeoka, Namiko Mitarai
Modeling slow-processing of toxin messenger RNAs in type-I Toxin-Antitoxin systems: post-segregational killing and noise filtering
BioRxiv 0 (2018)