News: Welcome to Šarūnė Ivanovaitė and Elmar van der Wijk

Šarūnė recently started her Erasmus+ internship in the group. She will characterise a variety of fluidic devices that we got our hands on including devices for high throughput smFRET screening, trapping of bacteria and establishing DNA curtains. Elmar started his MSc thesis and will utilise new DNA constructs for smFRET based studies of ARF transcription factor binding.

Pre-print: Design principles of a minimal auxin response system

H. Kato, S.K. Mutte, H. Suzuki, I.  Crespo, S.  Das, T. Radoeva, M. Fontana, Y. Yoshitake, E. Hainiwa, W. van den Berg, S. Lindhoud, J. Hohlbein, J.W. Borst, D.R. Boer, R. Nishihama, T. Kohchi, D. Weijers, bioRxiv, 2019, [link]

Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. Expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned, or prevented. This fundamental design likely represents the ancestral system, and formed the basis for inflated, complex systems.



Publication: Visualisation of dCas9 target search in vivo using an open-microscopy framework

K.J.A. Martens, S. van Beljouw, S. van der Els, J.N.A. Vink, S. Baas, G.A. Vogelaar, S.J.J. Brouns, P. van Baarlen, M. Kleerebezem, J. Hohlbein, Nature Communications, 10, 3552, 2019, [link]

CRISPR-Cas9 is widely used in genomic editing, but the kinetics of target search and its relation to the cellular concentration of Cas9 have remained elusive. Effective target search requires constant screening of the protospacer adjacent motif (PAM) and a 30 ms upper limit for screening was recently found. To further quantify the rapid switching between DNA-bound and freely-diffusing states of dCas9, we developed an open-microscopy framework, the miCube, and introduce Monte-Carlo diffusion distribution analysis (MC-DDA). Our analysis reveals that dCas9 is screening PAMs 40% of the time in Gram-positive Lactoccous lactis, averaging 17 ± 4 ms per binding event. Using heterogeneous dCas9 expression, we determine the number of cellular target-containing plasmids and derive the copy number dependent Cas9 cleavage. Furthermore, we show that dCas9 is not irreversibly bound to target sites but can still interfere with plasmid replication. Taken together, our quantitative data facilitates further optimization of the CRISPR-Cas toolbox.



News: Welcome to Abbas Jabermoradi, Ben Tumulero, Vincent Boerkamp, and Sven Koens

Great to see so many people joining the group. Abbas started his PhD thesis on super-resolution based localisation of biomolecules at food-related interfaces. Ben (BSc thesis, BIP) started illuminating bacteria using the PAINT technique. Vincent (MSc thesis, BIP) supports Koen in his quest to monitor particle diffusion in meat replacers. Last but not least, Sven (BSc thesis with BIC & BIP) will study the influence of control elements to the transcription factor binding.

Some PAINT data by Ben


Pre-print: Direct visualization of native CRISPR target search in live bacteria reveals Cascade DNA surveillance mechanism

J.N.A. Vink, K.J.A. Martens, M. Vlot, R.E. McKenzie, C. Almendros, B. Estrada Bonilla, D.J.W. Brocken, J. Hohlbein, S.J.J. Brouns, bioRxiv, 2019, [link]

CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here we visualized individual Cascade complexes in a native type I CRISPR-Cas system. We uncovered an exponential relationship between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and impact CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.


Published: Evaluating single-particle tracking by photo-activation localization microscopy (sptPALM) in Lactococcus lactis

S.P.B. van Beljouw, S. van der Els, K.J. A. Martens, M. Kleerebezem, P.A. Bron, J. Hohlbein, Physical Biology, 16, 035001, 2019, [link]

Lactic acid bacteria (LAB) are frequently used in food fermentation and are invaluable for the taste and nutritional value of the fermentation end-product. To gain a better understanding of underlying biochemical and microbiological mechanisms and cell-to-cell variability in LABs, single-molecule techniques such as single-particle tracking photo-activation localization microscopy (sptPALM) hold great promises but are not yet employed due to the lack of detailed protocols and suitable assays.

Here, we qualitatively test various fluorescent proteins including variants that are photoactivatable and therefore suitable for sptPALM measurements in Lactococcus lactis, a key LAB for the dairy industry. In particular, we fused PAmCherry2 to dCas9 allowing the successful tracking of single dCas9 proteins, whilst the dCas9 chimeras bound to specific guide RNAs retained their gene silencing ability in vivo. The diffusional information of the dCas9 without any targets showed different mechanistic states of dCas9: freely diffusing, bound to DNA, or transiently interacting with DNA. The capability of performing sptPALM with dCas9 in L. lactis can lead to a better, general understanding of CRISPR-Cas systems as well as paving the way for CRISPR-Cas based interrogations of cellular functions in LABs.

screenshot 2019-01-24 at 09.23.00