title: Cell-Like Nanostructured Environments Alter Diffusion and Reaction Kinetics in Cell-Free Gene Expression.
abstract: In highly crowded and viscous intracellular environments, the kinetics of complex enzymatic reactions are determined by both reaction and diffusion rates. However in vitro studies on transcription and translation often fail to take into account the density of the prokaryotic cytoplasm. Here we mimic the cellular environment by using a porous hydrogel matrix, to study the effects of macromolecular crowding on gene expression. We found that within microgels gene expression is localized, transcription is enhanced up to fivefold, and translation is enhanced up to fourfold. Our results highlight the need to consider the role of the physical environment on complex biochemical reactions, in this case macromolecular crowding, nanoscale spatial organization, and confinement.
authors.affiliation: Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands.
authors.forename: Maike M K
authors.initials: MM
authors.lastname: Hansen
authors.affiliation: Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands.|Rhine-Waal University of Applied Sciences, Marie-Curie-Strasse 1, 47533, Kleve, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Paffenholz
authors.affiliation: Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands.
authors.forename: David
authors.initials: D
authors.lastname: Foschepoth
authors.affiliation: Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands.
authors.forename: Hans A
authors.initials: HA
authors.lastname: Heus
authors.affiliation: Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands. thiele@ipfdd.de.|Department of Nanostructured Materials and, Leibniz Research Cluster (LRC), Leibniz-Institut für Polymerforschung Dresden e. V., Hohe Strasse 6, 01069, Dresden, Germany. thiele@ipfdd.de.
authors.forename: Julian
authors.initials: J
authors.lastname: Thiele
authors.affiliation: Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands. w.huck@science.ru.nl.
authors.forename: Wilhelm T S
authors.initials: WT
authors.lastname: Huck
mesh_terms: D004247:DNA / Q000378:metabolism; D004058:Diffusion; D036681:Fluorescence Recovery After Photobleaching; D020100:Hydrogels / Q000737:chemistry; D007700:Kinetics; D046210:Microfluidic Analytical Techniques; D049329:Nanostructures / Q000737:chemistry*; D016062:Porosity; D014176:Protein Biosynthesis; D011506:Proteins / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D020100:Hydrogels; D011506:Proteins; D004247:DNA
keywords: crowding; fluorescent probes; gene expression; hydrogel; microfluidics; spatial localization