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Bert Poolman  - - - 
Top co-authors See all
Arnold J.M. Driessen

391 shared publications

Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands

Oscar P Kuipers

282 shared publications

Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands

Siewert J. Marrink

199 shared publications

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands

Bas Teusink

139 shared publications

Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

Gary J. Pielak

123 shared publications

Department of ChemistryUniversity of North Carolina Chapel Hill North Carolina, 27599

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Distribution of Articles published per year 
(1996 - 2018)
Total number of journals
published in
 
30
 
Publications See all
Article 0 Reads 0 Citations Conformational and dynamic plasticity in substrate-binding proteins underlies selective transport in ABC importers Marijn De Boer, Giorgos Gouridis, Ruslan Vietrov, Stephanie ... Published: 22 March 2019
eLife, doi: 10.7554/elife.44652
DOI See at publisher website PubMed View at PubMed ABS Show/hide abstract
Substrate-binding proteins (SBPs) are associated with ATP-binding cassette importers and switch from an open to a closed conformation upon substrate binding, providing specificity for transport. We investigated the effect of substrates on the conformational dynamics of six SBPs and the impact on transport. Using single-molecule FRET, we reveal an unrecognized diversity of plasticity in SBPs. We show that a unique closed SBP conformation does not exist for transported substrates. Instead, SBPs sample a range of conformations that activate transport. Certain non-transported ligands leave the structure largely unaltered or trigger a conformation distinct from that of transported substrates. Intriguingly, in some cases, similar SBP conformations are formed by both transported and non-transported ligands. In this case, the inability for transport arises from slow opening of the SBP or the selectivity provided by the translocator. Our results reveal the complex interplay between ligand-SBP interactions, SBP conformational dynamics and substrate transport.
Article 0 Reads 0 Citations Decreased Effective Macromolecular Crowding in Escherichia coli Adapted to Hyperosmotic Stress Boqun Liu, Zarief Hasrat, Bert Poolman, Arnold J. Boersma Published: 04 March 2019
Journal of Bacteriology, doi: 10.1128/jb.00708-18
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Escherichia coli adapts to changing environmental osmolality to survive and maintain growth. It has been shown that GFP diffusion in cells adapted to osmotic upshifts is higher than expected from the increase in biopolymer volume fraction. To better understand the physicochemical state of the cytoplasm in adapted cells, we now follow the macromolecular crowding during adaptation with FRET-based sensors. We apply an osmotic upshift and find that, after an initial increase, the apparent crowding decreases over the course of hours, to arrive at a value lower than before the osmotic upshift. Crowding relates to cell volume until cell division ensues, after which a transition in the biochemical organization occurs. Analysis of single cells by microfluidics shows that changes in cell volume, elongation and division are most likely not the cause for the transition in organization. We further show that the decrease in apparent crowding upon adaptation is similar to the apparent crowding in energy-depleted cells. Based on our findings in combination with literature data, we suggest that adapted cells have indeed an altered biochemical organization of the cytoplasm, possibly due to different effective particle-size distributions and concomitant nanoscale heterogeneity. This could potentially be a general response to accommodate higher biopolymer fractions yet retaining crowding homeostasis, and could apply to other species or conditions as well. IMPORTANCE Bacteria adapt to ever changing environmental conditions such as osmotic stress and energy limitation. It is not well understood how biomolecules reorganize themselves inside Escherichia coli under these conditions. An altered biochemical organization would affect macromolecular crowding, which could influence reaction rates and diffusion of macromolecules. In cells adapted to osmotic upshift, protein diffusion is indeed faster than expected on the basis of the biopolymer volume fraction. We now probe the effects of macromolecular crowding in cells adapted to osmotic stress or depleted in metabolic energy with a genetically encoded fluorescence-based probe. We find that the effective macromolecular crowding in adapted and energy-depleted cells is lower than in unstressed cells, indicating major alterations in the biochemical organization of the cytoplasm.
Article 0 Reads 0 Citations Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength Claire E. Price, Filipe Branco Dos Santos, Anne Hesseling, J... Published: 10 January 2019
BMC Evolutionary Biology, doi: 10.1186/s12862-018-1331-x
DOI See at publisher website PubMed View at PubMed ABS Show/hide abstract
A central theme in (micro)biology is understanding the molecular basis of fitness i.e. which strategies are successful under which conditions; how do organisms implement such strategies at the molecular level; and which constraints shape the trade-offs between alternative strategies. Highly standardized microbial laboratory evolution experiments are ideally suited to approach these questions. For example, prolonged chemostats provide a constant environment in which the growth rate can be set, and the adaptive process of the organism to such environment can be subsequently characterized. We performed parallel laboratory evolution of Lactococcus lactis in chemostats varying the quantitative value of the selective pressure by imposing two different growth rates. A mutation in one specific amino acid residue of the global transcriptional regulator of carbon metabolism, CcpA, was selected in all of the evolution experiments performed. We subsequently showed that this mutation confers predictable fitness improvements at other glucose-limited growth rates as well. In silico protein structural analysis of wild type and evolved CcpA, as well as biochemical and phenotypic assays, provided the underpinning molecular mechanisms that resulted in the specific reprogramming favored in constant environments. This study provides a comprehensive understanding of a case of microbial evolution and hints at the wide dynamic range that a single fitness-enhancing mutation may display. It demonstrates how the modulation of a pleiotropic regulator can be used by cells to improve one trait while simultaneously work around other limiting constraints, by fine-tuning the expression of a wide range of cellular processes. The online version of this article (10.1186/s12862-018-1331-x) contains supplementary material, which is available to authorized users.
Article 0 Reads 0 Citations How Important Is Protein Diffusion in Prokaryotes? Paul E. Schavemaker, Arnold J. Boersma, Bert Poolman Published: 13 November 2018
Frontiers in Molecular Biosciences, doi: 10.3389/fmolb.2018.00093
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That diffusion is important for the proper functioning of cells is without question. The extent to which the diffusion coefficient is important is explored here for prokaryotic cells. We discuss the principles of diffusion focusing on diffusion-limited reactions, summarize the known values for diffusion coefficients in prokaryotes and in in vitro model systems, and explain a number of cases where diffusion coefficients are either limiting for reaction rates or necessary for the existence of phenomena. We suggest a number of areas that need further study including expanding the range of organism growth temperatures, direct measurements of diffusion limitation, expanding the range of cell sizes, diffusion limitation for membrane proteins, and taking into account cellular context when assessing the possibility of diffusion limitation.
Article 0 Reads 0 Citations (Membrane) Protein Production in Context Paul E. Schavemaker, Bert Poolman Published: 01 November 2018
Trends in Biochemical Sciences, doi: 10.1016/j.tibs.2018.08.009
DOI See at publisher website
Article 0 Reads 1 Citation Method for immobilization of living and synthetic cells for high-resolution imaging and single-particle tracking Ɓukasz Syga, Dian Spakman, Christiaan M. Punter, Bert Poolma... Published: 13 September 2018
Scientific Reports, doi: 10.1038/s41598-018-32166-y
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Super-resolution imaging and single-particle tracking require cells to be immobile as any movement reduces the resolution of the measurements. Here, we present a method based on APTES-glutaraldehyde coating of glass surfaces to immobilize cells without compromising their growth. Our method of immobilization is compatible with Saccharomyces cerevisiae, Escherichia coli, and synthetic cells (here, giant-unilamellar vesicles). The method introduces minimal background fluorescence and is suitable for imaging of single particles at high resolution. With S. cerevisiae we benchmarked the method against the commonly used concanavalin A approach. We show by total internal reflection fluorescence microscopy that modifying surfaces with ConA introduces artifacts close to the glass surface, which are not present when immobilizing with the APTES-glutaraldehyde method. We demonstrate validity of the method by measuring the diffusion of membrane proteins in yeast with single-particle tracking and of lipids in giant-unilamellar vesicles with fluorescence recovery after photobleaching. Importantly, the physical properties and shape of the fragile GUVs are not affected upon binding to APTES-glutaraldehyde coated glass. The APTES-glutaraldehyde is a generic method of immobilization that should work with any cell or synthetic system that has primary amines on the surface.
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