Biology subjects

Halliday, K.

Publications and source records attributed to Halliday, K..

10 recordsLinked to original sources

bioRxiv2025

PHYTOCHROME INTERACTING FACTOR 7 moderates the activity and the cytosolic-nuclear shuttling of PHYTOCHROME A

In nature, plants perceive and respond to complex vegetative environments through the phytochrome (phy) photoreceptor-signaling system. The canopy adaptation strategy, elicited by phyA, together with the shade avoidance syndrome, regulated by phyB, enables plants to adapt to diverse forms of vegetation shade. The phyA High Irradiance Response (HIR) mode, which involves photocycle-coupled nuclear shuttling, is essential for sensing sustained far-red rich conditions typical of canopy or occlusive shade. Our research identifies PHYTOCHROME INTERACTION FACTOR 7 (PIF7) as a key regulator of phyA function. We show that PIF7ox effectively suppresses phyA action. Under persistent shade, PIF7 and phyA both accumulate and interact within nuclear photobodies, with binding mediated by the C-terminal domain of PIF7 and the PAS-PAS domain of phyA. PIF7 also interacts with FHY1 and FHL transport facilitators, thereby interfering with phyA cytosolic-nuclear shuttling. This coordinated molecular targeting by PIF7 constitutes an effective strategy for modulating phyA function under shaded conditions.

plant biology↗

bioRxiv2025

From Photoperiod Thresholds to Photoperiod sensitivity: Dual Strategies for Cost-Effective Speed Breeding and Climate-Ready Barley

Yield and the duration of the growing season are closely linked. Climate change may shorten growing seasons in certain European regions, and reducing the time to flowering could be an effective strategy to mitigate its effects. Therefore, exploring allelic combinations shape flowering time, is needed. Additionally, speed breeding (SB), characterized by extended photoperiods to accelerate generation time, can be energy-intensive, and the shortest day length needed to induce rapid flowering remains unknown. We present the first integrated study of how allelic variation at three key flowering time genes, PPD-H1, ELF3 and PHYC, modulates three parameters of the photoperiod response model: threshold photoperiod, photoperiod sensitivity, and intrinsic earliness. We recorded flowering under lengths of 16-24h in Near Isogenic Lines carrying PhyC-e or PhyC-I allele within ppd-H1 background, and in lines from HEB-25 combining wild and domesticated alleles of ELF3 and PPD-H1. The ELF3 allele in ppd-H1 background reduced intrinsic earliness, whereas PhyC-e reduced photoperiod sensitivity, opening opportunities for climate change adaptation. Remarkably, ppd-H1 lines flowered at a 20-h threshold, whereas Ppd-H1 lines showed no response, consequently we propose new SB photoperiods at 20 and 16h depending on PPD-H1 background. These photoperiods lower energy costs compared to the current 22h standard. HighlightsBy studying barley key photoperiod response genes, our results support energy-efficient speed breeding and the development of climate-resilient varieties through targeted genetic control of flowering time.

plant biology↗

bioRxiv2025

Nanoscopic tau aggregates in Parkinson's disease

Post-mortem tau pathology is frequently observed in Parkinsons disease (PD) using immunohistochemistry (IHC) to measure large inclusions, however, small protein aggregates that precede inclusions are considered a major driver of toxicity in neurodegenerative disease. We aimed to uncover the distribution of nanoscopic aggregates across six brain regions in post-mortem tissue from 14 PD and 15 controls using the single-molecule pull-down assay (SiMPull). In the hippocampus and amygdala, tau IHC and SiMPull were associated with advanced age in controls and dementia status in PD. Despite negligible tau IHC-labelled aggregates in the putamen, we identified a unique population of high-intensity nanoscopic tau aggregates for a subset of PD cases using SiMPull, ranging from 10-1,000 epitopes per aggregate and 30-1,000 nm in length. Previous evidence linking nigrostriatal tau pathology and motor deficits indicates that the nanoscopic tau aggregates identified in this study may contribute to striatal dysfunction in PD.

neuroscience↗

bioRxiv2025

Arabidopsis thaliana Phytochrome A Sensory Properties in Canopy Shade

Canopy shade environments can negatively impact plant growth and survival. Phytochrome A (phyA) is essential for seedling adaptation to deep shade, yet its role under moderate natural canopy conditions remains unclear. By expressing a novel phyA-nanoLUC reporter in Arabidopsis thaliana, we quantify diurnal fluctuations in phyA and its induction by low red to far-red (R:FR) ratio, simulating canopy shade. We uncover a new key regulatory function for phyB, which increases phyA stability post-dawn in unshaded conditions and modulates expression of PHYA in low R:FR. Further, we demonstrate that beyond its role as a deep shade sensor, phyA is an adept sensor of canopy shade, capable of detecting a range of R:FR ratios across light intensities. Mathematical modelling demonstrates that this property arises from the dynamic features of the phyA HIR mode of action. Interestingly, phyA synthesis is strongly induced by subtle reductions in R:FR ratio, and is robust to light perturbation, suggesting the phyA-sensory module is configured to detect modest shade. Spectral data from natural shade habitats provides ecological context for our laboratory findings. Physiological analysis indicates that under canopy shade phyA promotes seedling de-etiolation, organises resource management and accelerates reproductive development. We propose that this suite of responses, termed the "canopy adaptation strategy", enhances survival chances under conditions where shade-avoidance strategies are maladaptive.

plant biology↗

bioRxiv2023

Investigating the genetic control of plant development under speed breeding conditions

Speed breeding is a powerful tool to accelerate breeding and research programmes by shortening generation time and has been widely adopted for a range of crop species. Despite its success and growing popularity with breeders the genetic basis of plant development under speed breeding remains unknown. In this study, we explored how genotypes respond in terms of developmental advancement under different photoperiod regimes in the context of speed breeding. A subset of the barley HEB-25 Nested Association Mapping population was evaluated for days to heading and maturity under two contrasting photoperiod conditions: 1) Speed Breeding (SB) consisting of 22 hours of light and 2 hours of darkness), and 2) Normal Breeding (NB) consisting of 16 hours of light and 8 hours of darkness. GWAS revealed that developmental responses under both conditions were largely controlled by two loci: PPDH-1 and ELF3. Allelic variants at these genes determine whether plants display early flowering and maturity under both NB and SB. At key QTL regions, domesticated alleles were associated with late flowering and maturity in NB and early flowering and maturity in SB, whereas wild alleles were associated with early flowering under both conditions. We hypothesise that this may be related to the dark dependent repression of PPD-H1 by ELF3 which might be more prominent in NB conditions. Furthermore, by comparing development under two contrasting photoperiod regimes, we were able to derive an estimate of plasticity for the two traits. Interestingly, plasticity in development was largely attributed to allelic variation at ELF3. Our results have important implications for our understanding and optimisation of speed breeding protocols particularly when incorporating genetics from wild relatives into breeding programmes and the design of breeding programmes to support the delivery of climate resilient crops.

plant biology↗

bioRxiv2023

The synergetic effect from the combination of different adsorption resins in batch and semi-continuous cultivations of S. cerevisiae cell factories to produce acetylated Taxanes precursors of the anticancer drug Taxol

In situ product recovery is an efficient way to intensify bioprocesses as it can perform adsorption of the desired natural products in the cultivation. However, it is common to use only one adsorbent (liquid or solid) to perform the product recovery. For this study, the use of an in situ product recovery method with three combined commercial resins (HP-20, XAD7HP and HP-2MG) with different chemical properties was performed. A new yeast strain of Saccharomyces cerevisiae was engineered using CRISPR Cas9 (strain EJ2) to deliver heterologous expression of oxygenated acetylated taxanes that are precursors of the anticancer drug Taxol (R) (paclitaxel). Microscale cultivations using a definitive screening design (DSD) were set to get the best resin combinations and concentrations to retrieve high taxane titers. Once the best resin treatment was selected by the DSD, semi-continuous cultivation in high throughput microscale was performed to increase the total taxanes yield up to 783 {+/-} 33 mg/L. The best T5-yl Acetate yield obtained was up to 95 {+/-} 4 mg/L, the highest titer of this compound ever reported by a heterologous expression. It was also observed that by using a combination of the resins in the cultivation, 8 additional uncharacterized taxanes were found in the gas chromatograms compared to the dodecane overlay method. Lastly, the cell-waste reactive oxygen species concentrations from the yeast were 1.5-fold lower in the resins treatment compared to the control with no adsorbent aid. The possible future implications of this method could be critical for bioprocess intensification, allowing the transition to a semi-continuous flow bioprocess. Further, this new methodology broadens the use of different organisms for natural product synthesis/discovery benefiting from clear bioprocess intensification advantages.

bioengineering↗

bioRxiv2021

PIF7 controls leaf cell proliferation through an AN3 substitution-repression mechanism

Plants are agile, plastic organisms, able to adapt to ever-changing circumstances. Responding to far-red (FR) wavelengths from nearby vegetation, shade-intolerant species elicit the adaptive Shade Avoidance Syndrome (SAS), characterised by elongated petioles, leaf hyponasty and smaller leaves. We utilised end-of-day FR (EODFR) treatments to interrogate molecular processes that underlie the SAS leaf response. Genetic analysis establishes PHYTOCHROME INTERACTING FACTOR 7 (PIF7) is required for EODFR-mediated constraint of leaf blade cell division, while EODFR mRNAseq data identified ANGUSTIFOLIA3 (AN3) as a potential PIF7 target. We show PIF7 can suppress AN3 transcription through a sequestering mechanism that prevents AN3 activation of its own expression. We also establish PIF7 and AN3 impose antagonistic control of gene expression via common cis-acting promoter motifs in several cell cycle regulator genes. EODFR triggers the molecular substitution of AN3 to PIF7 at G-box/PBE-box promoter regions, and a switch from promotion to repression of gene expression.

plant biology↗

bioRxiv2020

BrphyB is critical for rapid recovery to darkness in mature Brassica rapa leaves

Crop biomass and yield are tightly linked to how the light signaling network translates information about the environment into allocation of resources, including photosynthates. Once activated, the phytochrome (phy) class of photoreceptors signal and re-deploy carbon resources to alter growth, plant architecture, and reproductive timing. Brassica rapa has been used as a crop model to test for conservation of the phytochrome-carbon network. B. rapa phyB mutants have significantly decreased or absent CO2-stimulated growth responses in seedlings, and adult plants have reduced chlorophyll levels, photosynthetic rate, stomatal index, and seed yield. Here, we examine the transcriptomic response of adult wild-type and BrphyB leaves to darkening and recovery in light. Three days of darkness was sufficient to elicit a response in wild type leaves suggesting a shift from carbon fixation and nutrient acquisition to active redistribution of cellular resources. Upon a return to light, wild-type leaves appeared to transcriptionally return to a pre-darkness state restoring a focus on nutrient acquisition. Overall, BrphyB mutant plants have a similar response with key differences in genes involved in photosynthesis and light response which deviate from the wild type transcriptional dynamics. Genes targeted to the chloroplast are especially affected. Adult BrphyB mutant plants had fewer, larger chloroplasts, further linking phytochromes, chloroplast development, photosynthetic deficiencies and optimal resource allocation.

plant biology↗

bioRxiv2018

Dawn and photoperiod sensing by phytochrome A

In plants, light receptors play a pivotal role in photoperiod sensing, enabling them to track seasonal progression. Photoperiod sensing arises from an interaction between the plants endogenous circadian oscillator and external light cues. Here, we characterise the role of phytochrome A (phyA) in photoperiod sensing. Our meta-analysis of functional genomic datasets identified phyA as a principal transcriptional regulator of morning-activated genes, specifically in short photoperiods. We demonstrate that PHYA expression is under the direct control of the PHYTOCHROME INTERACTING FACTOR transcription factors, PIF4 and PIF5. As a result, phyA protein accumulates during the night, especially in short photoperiods. At dawn phyA activation by light results in a burst of gene expression, with consequences for anthocyanin accumulation. The combination of complex regulation of PHYA transcript and the unique molecular properties of phyA protein make this pathway a sensitive detector of both dawn and photoperiod.\n\nSignificance statementThe changing seasons subject plants to a variety of challenging environments. In order to deal with this, many plants have mechanisms for inferring the season by measuring the duration of daylight in a day. A number of well-known seasonal responses such as flowering are responsive to daylength or photoperiod. Here, we describe how the photoreceptor protein phytochrome A senses short photoperiods. This arises from its accumulation during long nights, as happens during winter, and subsequent activation by light at dawn. As a result of this response, the abundance of red anthocyanin pigments is increased in short photoperiods. Thus, we describe a mechanism underlying a novel seasonal phenotype in an important model plant species.

plant biology↗

bioRxiv2017

Time-resolved Interaction Proteomics of the Putative Scaffold Protein GIGANTEA in Arabidopsis thaliana

The large, plant-specific protein GIGANTEA (GI) is involved in many physiological processes, mediating rhythmic, post-translational regulation in part through circadian and light regulation of GI RNA expression. GI binds several proteins implicated in the circadian clock, the control of photoperiodic flowering, and abiotic stress responses, and has co-chaperone activity. By extension, further interaction partners might mediate the less well-understood roles of GI but the number and rhythmicity of these interactors is unknown. Here, we seek potential interactors in a time-specific manner, using quantitative proteomics from a time series study of transgenic Arabidopsis thaliana plants constitutively expressing an epitope-tagged GI protein. Previously-identified, direct and indirect interactors of GI were detected but no further F-box proteins related to known GI partners ZTL/FKF1/LKP2. The predominantly non-rhythmic, interacting proteins were implicated in protein folding or degradation, metabolism and chromatin modification, including a small set of partners shared with other clock-related proteins. A transcription factor homologue that we name CYCLING DOF FACTOR 6 (CDF6) was shown to interact both with GI and the ZTL/FKF1/LKP2 proteins and to control photoperiodic flowering. Our results indicate the biochemical pathways, beyond circadian and flowering regulation, that might be affected by GIGANTEAs rhythmic, post-translational control.\n\nSignificance StatementSignificance statement of up to two sentences of no more than 75 words total;\n\nThe GIGANTEA protein of Arabidopsis was known for circadian and flowering functions, mediated by the FKF1/LKP2/ZTL family of GI-interacting, F-box proteins, then for a co-chaperone activity of unknown scope. We performed time-resolved, interaction proteomics, identifying CDF6 (At1g26790) as a morning-specific GI interactor that controls flowering time. Unlike FKF1 and CDF proteins, most of the 240 candidate partners were not rhythmically enriched. They link GI to proteostasis and metabolic functions that might mediate GIs physiological functions.

plant biology↗