Biology subjects

Bayer, E. E.

Publications and source records attributed to Bayer, E. E..

6 recordsLinked to original sources

bioRxiv2026

A Multiscale Model of Collective Decision-Making in Hybrid Aspen Tree Tissues Describes Bud-Dormancy Break

The mechanisms underlying cellular coordination within tissues remain enigmatic. Most models focus on interactions between just two levels of organization - cell and tissue - and do not leverage data across deeper hierarchies that best represent living processes, with many spatial and temporal scales interacting. Integrating many scales, from molecular to cellular to tissular to organismal to populational, may be necessary to fully elucidate tissue function, especially in cases of sparse data at each level. Here, we investigate multiscale, robust regulation of tissue-level decision-making, using experimental studies of cold induced dormancy release in terminal buds of hybrid aspen trees as our case study. We develop a network model of terminal bud meristematic tissue, incorporating expression data from a key cold induced regulator gene, FLOWERING LOCUS T (FT1), which controls bud dormancy release, combined with data on variability in cell-to-cell communication controlled by FT1 mediated regulation of plasmodesmata. The model can explain dormancy breaking under constant temperature, but not variable temperature. We introduce constraints from organismal-level data and show how the presence of coordinated cellular interactions within individual plant tissues is necessary to reproduce data of population-level statistics. Our findings demonstrate how mechanisms of tissue function may be better constrained when data are used across more scales. They also hint at potential tantalizing new insights such as how tissue function might not be solely dictated bottom-up from molecular interactions, but also top-down from constraints imposed by the organismal and population context. Both implications illustrate the critical importance of incorporating cross-scale information processing in modeling biological decision-making. Significance StatementBiological hierarchies involve decision-making mediated via nested feedback loops. Data-informed modeling of this hierarchal complexity remains challenging. Here, we leverage unique features of plant biology - stationary growth, prolonged decision-making, and physical structure - to study multiscale dynamics determining cellular mechanisms of bud dormancy breaking in aspen trees. We examine how tissue function can be driven bottom-up from gene regulatory networks and top-down from organismal population-level statistics. Modeling experimental data collected at genetic, cellular, and organismal levels, reveals how population-level data allow constraining mechanisms of cellular coordination within individual plants when cellular data are sparse. Our findings demonstrate how multiscale methods can combat data sparsity and suggest new ways to study cellular coordination within organisms could be dictated by organismal population-level constraints.

synthetic biology↗

bioRxiv2023

Deep Learning-Based Prediction of A. thaliana's MCTP4 Structure and Exploration of Transmembrane Dynamics using Coarse-Grained Molecular Dynamics Simulations

Multiple C2 Domains and Transmembrane region Proteins (MCTPs) in plants have been identified as important functional and structural components of plasmodesmata cytoplasmic bridges, which are vital for cell-cell communication. MCTPs are endoplasmic reticulum (ER)-associated proteins which contain three to four C2 domains and two transmembrane regions. In this study, we created structural models of Arabidopsis MCTP4 ER-anchor transmembrane region (TMR) domain using several prediction methods based on deep learning (DL). This region, critical for driving ER association, presents a complex domain organization and remains largely unknown. Our study demonstrates that using a single deep-learning method to predict the structure of membrane proteins can be challenging. Our deep learning models presented three different conformations for the MCTP4 structure, provided by different deep learning methods, indicating the potential complexity of the proteins conformational landscape. For the first time, we used simulations to explore the behaviour of the TMR of MCTPs within the lipid bilayer. We found that the TMR of MCTP4 is not rigid, but can adopt various conformations including some not identified by deep learning tools. These findings underscore the complexity of predicting protein structures. We learned that combining different methods, such as deep learning and simulations, enhances our understanding of complex proteins.

bioinformatics↗

bioRxiv2022

PIF4/HEMERA-mediated daytime thermosensory growth requires the Mediator subunit MED14

While moderately elevated ambient temperatures do not trigger stress responses in plants, they do significantly stimulate the growth of specific organs through a process known as thermomorphogenesis. The basic helix-loop-helix transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) plays a central role in regulating thermomorphogenetic hypocotyl elongation in various plant species, including Arabidopsis thaliana. Although it is well known that PIF4 promotes plant thermosensory growth by activating genes involved in the biosynthesis and signaling of the phytohormone auxin, the detailed molecular mechanism of such transcriptional activation is not clear. Our previous studies demonstrated that HEMERA (HMR), a transcriptional co-activator of PIF4, promotes the thermo-induced expression of PIF4 target genes through its nine-amino-acid transactivation domain (9aaTAD). In this report, we investigate the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression. Through the characterization of various mutants of the Mediator complex, a tail subunit named MED14 is identified as an essential factor for thermomorphogenetic hypocotyl growth. MED14 is required for the thermal induction of PIF4 target genes but has a marginal effect on the levels of PIF4 and HMR. Further transcriptomic analyses confirm that the expression of numerous PIF4/HMR-dependent, auxin-related genes requires MED14 at warm temperatures. Moreover, PIF4 and HMR physically interact with MED14 and both are indispensable for the association of MED14 with the promoters of these thermoresponsive genes. Taken together, these results unveil an important thermomorphogenetic mechanism, in which PIF4 and HMR recruit the Mediator complex to activate auxin-related growth-promoting genes when plants sense moderate increases in ambient temperature. One-sentence summaryThe Mediator subunit MED14 promotes thermomorphogenesis by interacting with PHYTOCHROME-INTERACTING FACTOR 4 and HEMERA to induce the expression of growth-promoting genes at elevated temperatures.

plant biology↗

bioRxiv2021

The receptor kinase SRF3 coordinates iron-level and flagellin dependent defense and growth responses in plants

Iron is critical for host-pathogen interactions. While pathogens seek to scavenge iron to spread, the host aims at decreasing iron availability to reduce pathogen virulence. Thus, iron sensing and homeostasis are of particular importance to prevent host infection and part of nutritional immunity. While the link between iron homeostasis and immunity pathways is well established in plants, how iron levels are sensed and integrated with immune response pathways remain unknown. We identified a receptor kinase, SRF3 coordinating root growth, iron homeostasis and immunity pathways via regulation of callose synthase activity. These processes are modulated by iron levels and rely on SRF3 extracellular and kinase domain which tune its accumulation and partitioning at the cell surface. Mimicking bacterial elicitation with the flagellin peptide flg22 phenocopies SRF3 regulation upon low iron levels and subsequent SRF3-dependent responses. We propose that SRF3 is part of nutritional immunity responses involved in sensing external iron levels.

plant biology↗

bioRxiv2019

Plasma membrane associated Receptor Like Kinases relocalise to plasmodesmata in response to osmotic stress.

Plasmodesmata act as key elements in intercellular communication, coordinating processes related to plant growth, development and responses to environmental stresses. While many of the developmental, biotic and abiotic signals are primarily perceived at the plasma membrane (PM) by receptor proteins, plasmodesmata also cluster receptor-like activities and whether or not these two pathways interact is currently unknown.\n\nHere we show that specific PM-located Leucine-Rich-Repeat Receptor-Like-Kinases (LRR-RLKs), KIN7 and IMK2, which under optimal growth conditions are absented from plasmodesmata, rapidly relocate and cluster to the pores in response to osmotic stress. This process is remarkably fast, it is not a general feature of PM-associated proteins and is independent of sterol- and sphingolipid-membrane composition. Focusing on KIN7, previously reported to be involved in stress responses, we show that relocalisation upon mannitol depends on KIN7 phosphorylation. Loss-of-function mutation in KIN7 induces delay in lateral root (LR) development and the mutant is affected in the root response to mannitol stress. Callose-mediated plasmodesmata regulation is known to regulate LR development. We found that callose levels are reduced in kin7 mutant background with a root phenotype resembling ectopic expression of PdBG1, an enzyme that degrades callose at the pores. Both the LR and callose phenotypes can be complemented by expression of KIN7 -wild-type and -phosphomimic variants but not by KIN7 phosphodead mutant which fails to relocalise at plasmodesmata. Together the data indicate that re-organisation of RLKs to plasmodesmata is important for the regulation of callose and LR development as part of the plant response to osmotic stress.

plant biology↗

bioRxiv2018

Multiple C2 domains and Transmembrane region Proteins (MCTPs) tether membranes at plasmodesmata

AO_SCPLOWBSTRACTC_SCPLOWIn eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved unique MCS, the plasmodesmata intercellular pores, which combine endoplasmic reticulum (ER) - plasma membrane (PM) contacts with regulation of cell-to-cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remains unknown.\n\nHere we show that the Multiple C2 domains and Transmembrane region Protein (MCTP) family, key regulators of cell-to-cell signalling in plants, act as ER - PM tethers specifically at plasmodesmata. We report that MCTPs are core plasmodesmata proteins that insert into the ER via their transmembrane region whilst their C2 domains dock to the PM through interaction with anionic phospholipids. A mctp3/4 loss-of-function mutant induces plant developmental defects while MCTP4 expression in a yeast {Delta}tether mutant partially restores ER-PM tethering. Our data suggest that MCTPs are unique membrane tethers controlling both ER-PM contacts and cell-cell signalling.

plant biology↗