Biology subjects

Loefke, C.

Publications and source records attributed to Loefke, C..

8 recordsLinked to original sources

bioRxiv2025

Nuclear auxin signalling induces autophagy for developmental reprogramming

The phytohormone auxin is a central regulator of plant growth and development, traditionally known for mediating transcriptional reprogramming through the canonical TIR1/AFB-Aux/IAA signalling pathway. In this study, we reveal that auxin rapidly induces macroautophagy, a catabolic process critical for the removal and recycling of superfluous macromolecules. We demonstrate that natural auxin (IAA) triggers autophagy at physiological concentrations. Genetic and pharmacological analyses show that TIR1/AFB receptors and their adenylate cyclase activity are indispensable for autophagy induction. Furthermore, auxin-induced autophagy depends on transcription, highlighting its integration with the broader gene regulatory networks. Functionally, we show that auxin-induced autophagy is required for efficient developmental reprogramming and organogenesis in both root and shoots. Autophagy is induced at places of local auxin maxima and autophagy-deficient mutants exhibit delayed differentiation and retarded organ primordia progression at the meristematic zones. Together, our findings uncover a dual role for auxin in coordinating gene expression and autophagic clearance, thereby facilitating rapid and effective developmental transitions.

plant biology↗

bioRxiv2025

Cell-type specific autophagy in root hair forming cells is essential for salt stress tolerance in Arabidopsis thaliana

Autophagy is a vital cellular quality control pathway that enables plants to adapt to changing environments. By degrading damaged or unwanted components, autophagy maintains cellular homeostasis. While the organismal phenotypes of autophagy-deficient plants under stress are well-characterized, the contribution of cell-type-specific autophagy responses to whole-plant homeostasis remains poorly understood. Here, we show that root hair-forming cells (trichoblasts) of Arabidopsis thaliana exhibit higher autophagic flux than adjacent non-hair cells (atrichoblasts). This differential autophagy is genetically linked to cell fate determination during early development. Mutants disrupting trichoblast or atrichoblast identity lose the autophagy distinction between these cell types. Functional analyses reveal that elevated autophagy in trichoblasts is essential for sodium ion sequestration in vacuoles--a key mechanism for salt stress tolerance. Disrupting autophagy specifically in trichoblasts impairs sodium accumulation and reduces plant survival under salt stress. Conversely, cell-type-specific complementation restores both sodium sequestration and stress tolerance. Our findings uncover a cell-type-specific autophagy program in root hairs and demonstrate how developmental cues shape autophagy to enhance stress resilience. This work establishes a direct link between cell identity, autophagy, and environmental adaptation in plants.

plant biology↗

bioRxiv2024

Nonuple atg8 mutant provides genetic evidence for functional specialization of ATG8 isoforms in Arabidopsis thaliana

Autophagy sustains cellular health by recycling damaged or excess components through autophagosomes. It is mediated by conserved ATG proteins, which coordinate autophagosome biogenesis and selective cargo degradation. Among these, the ubiquitin-like ATG8 protein plays a central role by linking cargo to the growing autophagosomes through interacting with selective autophagy receptors. Unlike most ATG proteins, the ATG8 gene family is significantly expanded in vascular plants, but its functional specialization remains poorly understood. Using transcriptional and translational reporters in Arabidopsis thaliana, we revealed that ATG8 isoforms are differentially expressed across tissues and form distinct autophagosomes within the same cell. To explore ATG8 specialization, we generated the nonuple{Delta} atg8 mutant lacking all nine ATG8 isoforms. The mutant displayed hypersensitivity to carbon and nitrogen starvation, coupled with defects in bulk and selective autophagy as shown by biochemical and ultrastructural analyses. Complementation experiments demonstrated that ATG8A could rescue both carbon and nitrogen starvation phenotypes, whereas ATG8H could only complement carbon starvation. Proximity labeling proteomics further identified isoform-specific interactors under nitrogen starvation, underscoring their functional divergence. These findings provide genetic evidence for functional specialization of ATG8 isoforms in plants and lay the foundation for investigating their roles in diverse cell types and stress conditions.

plant biology↗

bioRxiv2024

Salicylic Acid restricts cell elongation and induces changes of vacuolar morphology and pH

The phytohormone salicylic acid (SA) is a key factor to balance plant defence as well as growth and development. While its role in plant defence has been investigated for decades, regulation of plant growth and development has only come into focus recently. It has been demonstrated that SA application inhibits growth independently of the established Non-expressor of Pathogenesis Related (NPR) receptors. However, the underlying mechanism of this growth inhibition on the cellular level remains largely elusive. Here we show that SA restricts cell elongation and induces changes of vacuolar morphology and pH. Rapidly upon SA application we observe homotypic vacuole fusion and a significant increase in vacuolar pH. These changes seem to be independent of the phytohormone auxin which has been reported to crosstalk with SA. By increasing vacuolar pH, SA directly impacts basic cellular functions such as vesicle trafficking or nutrient storage, leading eventually to cell size restriction and limited growth. Our results demonstrate an NPR-independent mechanism to attenuate growth, potentially allowing free resources to be relocated to withstand environmental stresses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/611645v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@af7652org.highwire.dtl.DTLVardef@1813f64org.highwire.dtl.DTLVardef@68e2e8org.highwire.dtl.DTLVardef@92a13_HPS_FORMAT_FIGEXP M_FIG C_FIG Salicylic Acid (SA) triggers a reduction in cell size and leads to a spherical vacuolar phenotype. This morphological change is accompanied by an increase in vacuolar pH, potentially due to the enhanced activity of a glycosylated SA (SAG) H+-antiporter and/or the inhibition of V-ATPase activity. In addition, SA disrupts the polarity of PIN2 auxin transporters, resulting in their uniform distribution across the cell membrane.

plant biology↗

bioRxiv2021

Endocytic Trafficking Promotes Vacuolar Enlargements for Fast Cell Expansion Rates in Plants

The vacuole has a space-filling function, allowing a particularly rapid plant cell expansion with very little increase in cytosolic content (Lofke et al., 2015; Scheuring et al., 2016; Dunser et al., 2019). Despite its importance for cell size determination in plants, very little is known about the mechanisms that define vacuolar size. Here we show that the cellular and vacuolar size expansions are coordinated. By developing a pharmacological tool, we enabled the investigation of membrane delivery to the vacuole during cellular expansion. Counterintuitively, our data reveal that endocytic trafficking from the plasma membrane to the vacuole is enhanced in the course of rapid root cell expansion. While this "compromise" mechanism may theoretically at first decelerate cell surface enlargements, it fuels vacuolar expansion and, thereby, ensures the coordinated augmentation of vacuolar occupancy in dynamically expanding plant cells.

plant biology↗

bioRxiv2020

A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress

Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the ER. Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control at the ER.

cell biology↗

bioRxiv2019

Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells

Somatic cells acclimate to changes in the environment by temporary reprogramming. Much has been learned about transcription factors that induce these cell-state switches in both plants and animals, but how cells rapidly modulate their proteome remains elusive. Here, we show rapid induction of autophagy during temporary reprogramming in plants triggered by phytohormones, immune and danger signals. Quantitative proteomics following sequential reprogramming revealed that autophagy is required for timely decay of previous cellular states and for tweaking the proteome to acclimate to the new conditions. Signatures of previous cellular programs thus persist in autophagy deficient cells, affecting cellular decision-making. Concordantly, autophagy deficient cells fail to acclimatize to dynamic climate changes. Similarly, they have defects in dedifferentiating into pluripotent stem cells, and redifferentiation during organogenesis. These observations indicate that autophagy mediates cell state switches that underlie somatic cell reprogramming in plants and possibly other organisms, and thereby promotes phenotypic plasticity.

plant biology↗

bioRxiv2017

Peripheral infrastructure vectors and an extended set of plant parts for the modular cloning system

Standardized DNA assembly strategies facilitate the generation of multigene constructs from collections of building blocks in plant synthetic biology. A common syntax for hierarchical DNA assembly following the Golden Gate principle employing Type IIs restriction endonucleases was recently developed, and underlies the Modular Cloning and GoldenBraid systems. In these systems, transcriptional units and/or multigene constructs are assembled from libraries of standardized building blocks, also referred to as phytobricks, in several hierarchical levels and by iterative Golden Gate reactions. This combinatorial assembly strategy meets the increasingly complex demands in biotechnology and bioengineering, and also represents a cost-efficient and versatile alternative to previous molecular cloning techniques. For Modular Cloning, a collection of commonly used Plant Parts was previously released together with the Modular Cloning toolkit itself, which largely facilitated the adoption of this cloning system in the research community. Here, a collection of approximately 80 additional phytobricks is provided. These phytobricks comprise e.g. modules for inducible expression systems, different promoters or epitope tags, which will increase the versatility of Modular Cloning-based DNA assemblies. Furthermore, first instances of a \"peripheral infrastructure\" around Modular Cloning are presented: While available toolkits are designed for the assembly of plant transformation constructs, vectors were created to also use coding sequence-containing phytobricks directly in yeast two hybrid interaction or bacterial infection assays. Additionally, DNA modules and assembly strategies for connecting Modular Cloning with Gateway Cloning are presented, which may serve as an interface between available resources and newly adopted hierarchical assembly strategies. The presented material will be provided as a toolkit to the plant research community and will further enhance the usefulness and versatility of Modular Cloning.

plant biology↗