Biology subjects

Locke, J. C. W.

Publications and source records attributed to Locke, J. C. W..

10 recordsLinked to original sources

bioRxiv2026

Regulatory architecture tunes gene expression noise in the plant heat shock response

Cells within the same tissue can respond differently to the same stress, yet how gene regulatory networks generate and control this variability remains unclear. Here, we show that cell-to-cell variation in the Arabidopsis heat shock response is coordinated across the heat shock regulon and that the distribution of responses is tuned by the underlying regulatory network. Imaging of an HSP70 promoter reporter revealed basal activity in a subset of root cells and heterogeneous induction after heat shock, with some cells remaining near pre-stress expression levels. Dual reporters showed strong coordination between independently integrated HSP70 reporter loci, consistent with substantial shared upstream regulatory variation. Single-nucleus RNA sequencing confirmed heterogeneous but coordinated activation of heat shock genes across root cell types. Stronger heat shock states at both ambient and heat stress temperatures were associated with a recurrent thermoprotective programme across root cell populations, whereas weak responders after heat shock were associated with distinct cell-type specific transcriptional programmes, including defence- and jasmonate-associated states in some root cell types. Stochastic modelling suggested that HSFA2-dependent amplification could broaden the distribution of HSP70 expression across cells. Consistent with this prediction, experiments showed that loss of HSFA2 reduced HSP70 induction and lowered cell-to-cell variability after controlling for differences in mean expression. Together, these results show that the plant heat shock network controls both the magnitude and distribution of stress-responsive gene expression across cells.

plant biology↗

bioRxiv2025

A BRC1-modulated switch in auxin transport accounts for the competition between Arabidopsis axillary buds

As part of their modular development, plants continuously adapt their shoot branching architecture according to environmental conditions. This occurs by regulating the activity of axillary buds established in each leaf axil. Whether a bud grows into a shoot depends partly on the presence of other active shoots, which can inhibit bud activation. This systemic coordination is proposed to be mediated by the transport network of the plant hormone auxin, with buds competing to establish sustained transport of auxin, termed canalised auxin transport, into the main stem. A second hormone, strigolactone, tunes this competition by influencing the removal of the PIN1 auxin export protein from the plasma membrane, and hence the dynamics of canalisation. Strigolactone also regulates the expression of another key regulatory hub, the bud-expressed transcription factor BRANCHED1 (BRC1). The interplay between auxin transport and BRC1 in regulating bud activity is poorly understood. Here, we investigate this interplay in the context of competition between buds, using Arabidopsis explants with two axillary buds as a minimal system. Using experimental data, we develop a mathematical model of bud-bud competition in which BRC1 influences the establishment of canalised auxin transport by regulating the basal rate of auxin efflux in buds. We identify single model parameters that plausibly correspond to the dual impact of strigolactone on BRC1 expression and PIN1. We show that modulating these two parameters reproduces the dynamics of bud growth and bud-bud competition observed in relevant mutants and treatments. Our model produces testable hypotheses, which we validate by generating a chimeric PIN1 auxin transporter with impaired strigolactone sensitivity, helping us uncouple the effects of strigolactone on PIN1 and BRC1. These results support the hypothesis that BRC1 influences local bud competitiveness by tuning the basal rate of auxin efflux in buds. Together with the systemic feedbacks in the auxin transport network, this enables plants to adjust dynamically the number and location of growing branches.

plant biology↗

bioRxiv2025

Plasticity and invariance of Arabidopsis inflorescence and floral shoot apical meristems in response to mineral nutrients

In many species, floral organ production is invariant while flower production rate can be plastic. This allows plants to adapt flower number to their environment whilst maintaining a constant flower structure. The CLAVATA/WUSCHEL feedback loop underpins both inflorescence (IM) and floral meristem (FM) activity, respectively responsible for flower and floral organ production. We explore how plasticity and invariance can differ between IM and FM in response to nutrient availability. FM size is less sensitive to changes in nutrients than IM size, and floral organ production is insensitive to these small size changes. However, clavata3 mutants display larger changes in FM size, approaching those observed in WT IM under nutrient change, with increased floral organ number. This suggests that invariant floral organ production requires that FM size undergoes limited changes in response to nutrients. Compared to the IM, in the FM, levels of cytokinin (CK) signaling are lower and CK signaling and WUSCHEL expression are less impacted by nutrient level. Through genetic perturbations, we show a reduced response of FMs to varying cytokinin levels. Our work shows one way that the balance between plasticity and invariance can be set differently in different contexts.

plant biology↗

bioRxiv2024

Environmental and molecular noise buffering by the cyanobacterial clock in individual cells

Circadian clocks enable organisms to anticipate daily cycles, while being robust to molecular and environmental noise. Here, we show how the cyanobacterial clock buffers genetic and environmental perturbations through its core phosphorylation loop. We first characterise single-cell clock dynamics in clock mutants using a microfluidics device that allows precise control of the microenvironment. We find known clock regulators are dispensable for clock robustness, whilst perturbations of the core clock reveal that the wild-type operates at a noise optimum that we can reproduce in a stochastic model of just the core phosphorylation loop. We then examine how the clock responds to noisy environments, including natural light conditions. The model accurately predicts how the clock filters out environmental noise, including fast light fluctuations, to keep time while remaining responsive to environmental shifts. Our findings illustrate how a simple clock network can exhibit complex noise filtering properties, advancing our understanding of how biological circuits can perform accurately in natural environments.

systems biology↗

bioRxiv2023

The alternative sigma factor RpoD4 pulses at division and links the circadian clock and the cell cycle in Synechococcus elongatus

The cyanobacterial circadian clock is an extensive regulator of gene expression, generating a 24-hour rhythm in the majority of genes in Synechococcus elongatus PCC 7942. This raises the question of how the cyanobacterial clock regulates, and receives input from, the diverse cellular processes it controls. Alternative sigma factors, which bind to the core RNA polymerase enzyme and direct the synthesis of specific sets of transcripts, are one mechanism for the clock to set the time of its outputs. In this work, we use single-cell time-lapse microscopy to reveal the transcriptional dynamics of RpoD4, an alternative sigma factor that was previously reported as either arrhythmic or circadian. We find instead that RpoD4 pulses at cell division, dynamics missed by previous bulk averaging. The circadian clock modulates the amplitude of RpoD4 expression pulses, as well as the timing of pulses through its control of division timing. In turn, a rpoD4 mutation causes a reduction in clock period. Further, a rpoD4 mutant results in smaller cell size, and increasing expression of RpoD4 results in larger cell sizes in a dose-response manner, allowing tunable control of cell size. Thus, our single-cell analysis has revealed pulsing gene expression dynamics in cyanobacteria, linking the clock, RpoD4 and the cell cycle.

systems biology↗

bioRxiv2020

Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit

Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in B. subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history, and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗

bioRxiv2019

Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana

Every plant cell has a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we examined the clock at the sub-tissue level across Arabidopsis thaliana seedlings under multiple environmental conditions and genetic backgrounds. Our results show that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark cycles. Closer examination reveals that spatial waves of clock gene expression propagate both within and between organs. Using a combination of modeling and experiment, we reveal that these spatial waves are the result of the period differences between organs and local coupling, rather than long distance signaling. With further experiments we show that the endogenous period differences, and thus the spatial waves, are caused by the organ specificity of inputs into the clock. We demonstrate this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Our results reveal that plant clocks are set locally by organ specific inputs, but coordinated globally via spatial waves of clock gene expression.

plant biology↗

bioRxiv2017

Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression

The Arabidopsis circadian clock orchestrates gene regulation across the day/night cycle. Although a multiple feedback loop circuit has been shown to generate the 24h rhythm, it remains unclear how robust the clock is in individual cells, or how clock timing is coordinated across the plant. Here we examine clock activity at the single cell level across Arabidopsis seedlings over several days. Our data reveal robust single cell oscillations, albeit desynchronised. In particular, we observe two waves of clock activity; one going down, and one up the root. We also find evidence of cell-to-cell coupling of the clock, especially in the root tip. A simple model shows that cell-to-cell coupling and our measured period differences between cells can generate the observed waves. Our results reveal the spatial structure of the plant circadian clock and suggest that unlike the centralised mammalian clock, the clock has multiple points of coordination in Arabidopsis.

systems biology↗

bioRxiv2017

Nitrate modulates stem cell dynamics by regulating WUSCHEL expression through cytokinins

The shoot apical meristem (SAM) is responsible for the generation of all of the aerial parts of plants1. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment2. Using quantitative microscopy, grafting experiments and genetic perturbations, we connect the plant environment to the SAM, by describing the molecular mechanism by which cytokinins signal the level of nutrient availability to the SAM. We show that a systemic signal of cytokinin precursors3 mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of WUSCHEL, a key regulator of stem cell homeostasis4. In time-lapse experiments, we further show that this mechanism allows meristems to adapt to rapid changes in nitrate concentration, and thereby modulate their rate of organ production to the availability of mineral nutrients within a few days. Our work sheds new light on the role of the stem cell regulatory network, by showing that it does not only maintain meristem homeostasis but also allows plants to adapt to rapid changes in the environment.

plant biology↗

bioRxiv2017

Cell size control driven by the circadian clock and environment in cyanobacteria

How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-hour circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behaviour emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on-off gate to division as previously proposed. Iterating between modelling and experiments, we go on to show that the combined effects of the environment and the clock on cell division are explained by an effective coupling function. Under naturally graded light-dark cycles, this coupling shifts cell division away from dusk and dawn, when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.

systems biology↗