Biology subjects

Middelkoop, T. C.

Publications and source records attributed to Middelkoop, T. C..

4 recordsLinked to original sources

bioRxiv2023

Governing principles of transcriptional logic out of equilibrium

Cells face a myriad of environments and signaling cues. In order to survive, adapt, and desvelop, cells respond to external and internal stimuli, by tightly regulating transcription. Transcriptional regulation involves combinatorial binding of a repertoire of transcription factors (TFs) to DNA, which often results in switch-like binary outputs, akin to logic gates. Recent experimental studies have demonstrated that transcription factor binding to DNA often involves energy expenditure, thereby driving the system out of equilibrium. The governing mechanistic principles of transcriptional logic out of equilibrium remain elusive. To this end, we employ a simple two-input model of transcription that explicitly considers the non-equilibrium binding of TFs to DNA. This simple model can accommodate both equilibrium and non-equilibrium mechanisms and allows for a comparative study of logic operations obtained in the two regimes. We find that, out of equilibrium, the regulatory function of two transcription factors gets altered in a mutually exclusive manner. Such behavior allows non-equilibrium regimes to recreate all the logic operations seen in equilibrium and create new logic operations inaccessible in equilibrium. Our findings demonstrate that cells attain a wider range of decision-making abilities by expending energy.

biophysics↗

bioRxiv2023

A cytokinetic ring-driven cell rotation achieves Hertwig's rule in early development

Cells tend to divide along the direction in which they are longest, as famously stated by Oscar Hertwig in 1884 in his long axis rule1,2. The orientation of the mitotic spindle determines the cell division axis3, and Hertwigs long axis rule is usually ensured by forces stemming from microtubules4. Pulling on the spindle from the cell cortex can give rise to unstable behaviors5,6, and we here set out to understand how Hertwigs long axis rule is realized in early embryonic divisions where cortical pulling forces are prevalent. We focus on early C. elegans development, where we compressed embryos to reveal that cortical pulling forces favor an alignment of the spindle with the cells short axis. Strikingly, we find that this misalignment is corrected by an actomyosin-based mechanism that rotates the entire cell, including the mitotic spindle. We uncover that myosin-driven contractility in the cytokinetic ring generates inward forces that align it with the short axis, and thereby the spindle with the long axis. A theoretical model together with experiments using slightly compressed mouse zygotes suggest that a constricting cytokinetic ring can ensure Hertwigs long axis rule in cells that are free to rotate inside a confining structure, thereby generalizing the underlying principle.

developmental biology↗

bioRxiv2021

CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left-right symmetry breaking

1Proper left-right symmetry breaking is essential for animal development and in many species the actin cytoskeleton plays an instrumental role in this process. Active torque generation in the actomyosin layer promotes left-right symmetry breaking in C. elegans embryos by driving chiral counter-rotating cortical flows. While both Formins and Myosins have been implied in left-right symmetry breaking, and both can rotate actin filaments in vitro, it remains unclear if active torques in the actomyosin cortex are generated by Formins, Myosins, or both. We combined the strength of C. elegans genetics with quantitative imaging and thin film, chiral active fluid theory to show that, while Non-Muscle Myosin II activity drives cortical actomyosin flows, it is permissive for chiral counter-rotation and dispensable for chiral symmetry breaking of cortical flows. Instead, we find that CYK-1/Formin activation in RhoA foci is instructive for chiral counter-rotation and promotes in-plane, active torque generation in the actomyosin cortex. Notably, we observe that artificially generated large active RhoA patches undergo rotations with consistent handedness in a CYK-1/Formin-dependent manner. Altogether, we conclude that, CYK-1/Formin-dependent active torque generation facilitates chiral symmetry breaking of actomyosin flows and drives organismal left-right symmetry breaking in the nematode worm. 2 SignificanceActive torque generation in the actin cytoskeleton has been implicated in driving left-right symmetry breaking of developing embryos, but which molecules generate the active torque and how active torque generation is organized subcellularly remains unclear. This study shows that cortical Formin, recruited to cortical regions where RhoA signaling is active, promotes active torque generation in the actomyosin layer. We find that active torque tends to locally rotate the cortex in a clockwise fashion, which drives the emergence of chiral counter-rotating flows with consistent handedness and facilitates left-right symmetry breaking of C. elegans embryos.

developmental biology↗

bioRxiv2019

Cell lineage-dependent chiral actomyosin flows drive cellular rearrangements in early development

Proper positioning of cells is important for many aspects of embryonic development, tissue homeostasis, and regeneration. A simple mechanism by which cell positions can be specified is via orienting the cell division axis. This axis is specified at the onset of cytokinesis, but can be reoriented as cytokinesis proceeds. Rotatory actomyosin flows have been implied in specifying and reorienting the cell division axis in certain cases, but how general such reorientation events are, and how they are controlled, remains unclear. In this study, we set out to address these questions by investigating early Caenorhabditis elegans development. In particular, we determined which of the early embryonic cell divisions exhibit chiral counter-rotating actomyosin flows, and which do not. We follow the first nine divisions of the early embryo, and discover that chiral counter-rotating flows arise systematically in the early AB lineage, but not in early P/EMS lineage cell divisions. Combining our experiments with thin film active chiral fluid theory we identify specific properties of the actomyosin cortex in the symmetric AB lineage divisions that favor chiral counter-rotating actomyosin flows of the two halves of the dividing cell. Finally, we show that these counter-rotations are the driving force of both the AB lineage spindle skew and cell reorientation events. In conclusion, we here have shed light on the physical basis of lineage-specific actomyosin-based processes that drive chiral morphogenesis during development.

cell biology↗