Biology subjects

Bauer, P.

Publications and source records attributed to Bauer, P..

At least 19 recordsLinked to original sources

bioRxiv2026

FE DEFICIENCY-INDUCED KELCH REPEAT PROTEIN 1 (FDK1) links coumarin metabolism and iron homeostasis during alkaline iron deficiency in Arabidopsis

Although iron (Fe) is abundant in soils, its low solubility, particularly under alkaline conditions, often limits plant Fe acquisition. Under these conditions, coumarin-mediated Fe mobilization becomes increasingly important. Arabidopsis thaliana FE DEFICIENCY-INDUCED KELCH REPEAT PROTEIN 1 (FDK1, AT3G07720) is strongly induced by Fe deficiency and regulated by the central transcription factor FIT, but its function is unknown. We investigated FDK1 using genetic, physiological, metabolite, and transcriptomic analyses. Loss of FDK1 altered root growth, whereas this phenotype was restored in the FDK1-Ox overexpression line. Under alkaline Fe deficiency, growth medium from FDK1-Ox contained strongly increased levels of the Fe-mobilizing coumarins fraxetin and esculetin compared with wild type, whereas their induction was attenuated in fdk1-1. RNA-seq analysis linked FDK1 abundance to coumarin biosynthesis and iron-homeostasis gene expression. FIT and many FIT-associated genes were highly expressed in FDK1-Ox, whereas several upstream iron-homeostasis regulators, including bHLH Ib factors, were highest in fdk1-1. These findings identify FDK1 as a component of the alkaline Fe-deficiency response that promotes iron-mobilizing coumarin accumulation and is associated with coordinated regulation of iron-homeostasis genes.

plant biology↗

bioRxiv2026

Dorsal ocelli set the luminance-dependent operating state of the bumblebee visual system

Despite long-standing hypotheses that insect dorsal ocelli modulate compound-eye processing to support flight stabilization, dim-light navigation, and locomotor speed, the neurophysiological basis of these functions remains unclear. Combining behavioural assays with multi-site local field potential recordings in bumblebees, we tested how ocellar input affects compound-eye processing. Ocellar occlusion impaired orientation precision at dusk, supporting a role for ocelli in dim-light navigation. Under bright daytime skies, occlusion did not affect orientation but reduced flight speed, consistent with a role in locomotor control under high illumination. Neurophysiologically, ocellar occlusion disrupted luminance-dependent scaling across the visual system, most prominently in the medulla. In intact bees, broadband neural power scaled inversely with luminance, decreasing under bright and increasing under dim conditions. When ocellar input was blocked, this relationship reversed, leaving visual-system activity in a high-power, dark-like state even under bright illumination. Ocellar modulation was particularly evident in the green-sensitive pathway, implicated in optic-flow processing and flight-speed regulation, providing a neural correlate of the behavioural speed reduction while UV-sensitive responses remained largely invariant following ocellar occlusion. These findings reconcile disparate views of ocellar function and identify ocelli as regulators of the neural dynamic range supporting orientation in low light and movement control in bright conditions.

neuroscience↗

bioRxiv2025

A three amino acid sequence gates protein stability control of bHLH104 and iron uptake in Arabidopsis thaliana

Iron (Fe) homeostasis is regulated to prevent iron imbalance, with the help of redundant basic helix-loop-helix (bHLH) IVc transcription factors that can be controlled by Fe-binding E3 ligases such as BRUTUS (BTS) in Arabidopsis thaliana. However, knowledge gaps remain to fully explain the mechanistic basis of this redundant protein interaction module. The C-terminus of bHLH104 interacts with BTS. Structural predictions suggest involvement of the three terminal amino acids, proline-alanine-alanine (PAA). However, the importance of the PAA short sequence for post-translational regulation of bHLH104 and resulting plant phenotypes has not been experimentally tested. Here, we demonstrate that transgenic plants expressing a bHLH104 variant lacking PAA (b104^dPAA) constitutively upregulated Fe acquisition and Fe transport genes and consequently accumulated Fe in contrast to wild-type bHLH104 protein-expressing plants. The extent of Fe accumulation in independent b104^dPAA lines correlated positively with b104^dPAA protein abundance. In contrast to the wild-type bHLH104 form, there was no indication that b104^dPAA interacted with BTS or was ubiquitinated by it. Together, these findings corroborated that the PAA sequence is required for post-translational control of bHLH104 by BTS. Hence, targeted manipulation of bHLHIVc protein PAA sequence may represent a strategy for crop biofortification. Plain language summaryPlants tightly control iron levels. In Arabidopsis thaliana, transcription factor bHLH104 steers iron uptake. E3 ligases like BTS regulate bHLH104. We show that a three-amino acid terminal sequence of bHLH104 is needed for its targeting by the BTS pathway. bHLH104 lacking PAA leads to iron accumulation. Targeting this short sequence can be a strategy for crop biofortification.

plant biology↗

bioRxiv2025

Balancing nutrient remobilization and photosynthesis: the dual role of lupin cotyledons after germination

Efficient nutrient mobilization from seed storage tissues is essential for seedling establishment, particularly in legumes such as Lupinus albus (white lupin), which thrive in nutrient-poor soils. This study investigates the role of cotyledons in nitrogen (N) and mineral remobilization after germination during their transition from storage organs to photosynthetically active tissues including the metabolic challenges posed by coexistence of these two functions in epigeal germination. We cultivated white lupin seedlings under nitrogen-deficient conditions, analyzing cotyledon composition and function over 28 days. Our results indicate that 60 % of cotyledon-stored proteins are degraded within the first eight days, with free amino acids transiently accumulating before being redistributed to support growth. The progressive depletion of cotyledon reserves was accompanied by structural and metabolic changes, including an increase in photosynthetic proteins. However, cotyledon photosynthetic capacity remained lower than that of true leaves, suggesting a transient role in energy metabolism. The loss of cotyledons before day 12 significantly impaired seedling development, emphasizing their critical contribution to nitrogen, phosphate, and micronutrient supply during early growth. Comparative proteomic analysis revealed dynamic shifts in nutrient transport, amino acid metabolism, and stress response pathways following cotyledon removal. These findings underscore the significance of cotyledon nutrient remobilization in legume adaptation to low-fertility soils and highlight potential targets for breeding strategies aimed at improving nutrient use efficiency. By optimizing cotyledon nutrient composition and function, future breeding efforts could enhance seedling vigor, reduce fertilizer dependency, and improve the nutritional value of lupin-based foods. Significance statementThis study uncovers how white lupin cotyledons balance nutrient storage and photosynthesis during early seedling development, ensuring sustained nitrogen and mineral supply under nutrient-deficient conditions. By detailing the proteome reorganization and consequences of premature cotyledon loss, it identifies key mechanisms supporting seedling resilience and adaptation to low-fertility soils.

plant biology↗

bioRxiv2025

Neuronal networks in the dorsal hippocampus causally regulate rescue behavior in mice

Prosocial behaviors, such as rescuing individuals in need, are crucial for social cohesion across species. While key brain regions involved in rescue behavior have been identified, the underlying neural mechanisms remain unclear. The hippocampus (HPC), known for its role in memory and spatial navigation, also contributes to emotional and social processing. However, its specific involvement in prosocial behavior is not well understood. Here, we investigate the causal role of the HPC in learning and executing rescue behavior in mice. Using chemogenetics, we show that the dorsal HPC (dHPC), but not the ventral HPC (vHPC), is essential for acquiring rescue behavior. Calcium imaging of the dHPC reveals network consolidation during successful rescues, with distinct synchronized ensembles and activity patterns linked to liberations of an individual in need. These findings establish a novel role for the dHPC in prosocial behavior, providing insights into the neural mechanisms underlying empathy-driven actions.

neuroscience↗

bioRxiv2025

PPM1M, a LRRK2-counteracting, phosphoRab12-preferring phosphatase with potential link to Parkinsons disease

Leucine-rich repeat kinase 2 (LRRK2) phosphorylates a subset of Rab GTPases that regulate receptor trafficking; activating mutations in LRRK2 are linked to Parkinsons disease. Rab phosphorylation is a transient event that can be reversed by phosphatases, including PPM1H, that acts on phosphoRab8A and phosphoRab10. Here we report a phosphatome-wide siRNA screen that identified PPM1M as a phosphoRab12-preferring phosphatase that also acts on phosphoRab8A and phosphoRab10. Upon knockout from cells or mice, PPM1M displays selectivity for phosphoRab12. As shown previously for mice harboring LRRK2 pathway mutations, knockout of Ppm1m leads to primary cilia loss in striatal cholinergic interneurons. We have also identified a rare PPM1M mutation in patients with Parkinsons disease that is catalytically inactive when tested in vitro and in cells. These findings identify PPM1M as a key player in the LRRK2 signaling pathway and provide a new therapeutic target for the possible benefit of patients with Parkinsons disease. TeaserParkinsons linked Rab phosphorylation is reversed by PPM1M; the inactive D440N variant is implicated in rare patient cases.

cell biology↗

bioRxiv2025

An affordable and non-invasive validated machine-aided phenotyping pipeline identifies phenotypic variation of stress resilience in alkaline calcareous soil across the life cycle in Arabidopsis thaliana

Alkaline calcareous soils (ACS) are prevalent globally and challenge plant growth by limiting nutrient uptake, such as iron. The model plant Arabidopsis thaliana thrives in disturbed urban environments wherein ACS conditions frequently occur. Existing research largely focused on vegetatively grown A. thaliana, while there is a notable lack of studies examining phenotypic variations across the life cycle in ACS. A valuable tool for understanding plant stress resilience is machine-aided phenotyping as it is non-invasive, rapid and accurate. But it is often unavailable to individual plant labs. Here, we established and validated an affordable MicroScan with PlantEye-based machine-aided phenotyping approach, collected and correlated quantitative growth data across plant life cycles in response to ACS. We used A. thaliana wild type and the chlorotic coumarin-deficient mutant f6h1-1 to assess weekly morphological and leaf color data both manually and using a multispectral PlantEye device. Through correlation analysis, we selected machine parameters to differentiate size and leaf chlorosis phenotypes. The correlation analysis indicated a close connection between rosette size and multiple spectral parameters, highlighting the importance of the rosette size for plant growth. Most reliable phenotyping was at the beginning bolting stage. This methodology further is validated to detect novel leaf chlorosis phenotypes of known iron deficiency mutants across growth stages. This affordable machine-aided phenotyping procedure is suitable for high-throughput accurate screening of small-grown rosette plants, such as A. thaliana, and enables the discovery of novel genetic and phenotypic variation during the life cycle for understanding plant resilience in challenging soil environments. Short summary sentenceA PlantEye machine-aided non-invasive accurate and reliable phenotyping pipeline depicted the importance of the rosette size for phenotyping and detected leaf chlorosis phenotypes of A. thaliana mutants across the life-cycle on alkaline calcareous soil. Highlights and major findings- A MicroScan PlantEye machine-aided non-invasive phenotyping pipeline was established for assessing growth data of A. thaliana across the life cycle on alkaline calcareous soil and distinguishing leaf chlorosis phenotypes. - Rosette size was found an important trait that characterizes A. thaliana growth. - Machine phenotyping was most reliable at the beginning bolting stage. - New phenotypes were detected for Fe homeostasis mutants.

plant biology↗

bioRxiv2024

Age-dependent differential iron deficiency responses of rosette leaves during reproductive stages in Arabidopsis thaliana

Iron (Fe) is essential for plant development throughout the life cycle. Rosette leaves are responsive to Fe supply in Arabidopsis thaliana. Little is known about the dynamics of Fe deficiency (-Fe) responses of rosette leaves during the reproductive stages. We studied the dynamics of Fe-dependent responses at four consecutive reproductive stages (rosette, bolting, flowering, mature silique stages, hereby named RS, BS, FS, MS). We examined the growth of rosette leaves, elemental contents and gene expression patterns of Fe homeostasis genes belonging to differently regulated groups. We determined individual leaf sizes during seven days of +Fe and -Fe treatment at the RS. Young leaves responded to -Fe with growth inhibition and yellowing. Old and young leaves differed in gene expression patterns and elemental contents. Differences were noted between the early and late reproductive stages (primarily RS and BS versus MS) and correlations between ionomic contents and gene expression were detected. All leaves had induced Fe recycling genes at -Fe. Our findings highlight a developmental stage-dependent modulation of +Fe and -Fe responses in leaves. We discuss possible leaf signaling mechanisms accounting for the distinct responses between old and young leaves. This insight is informative to strengthen our understanding on plant iron management. Highlight/ One-sentence summaryThis study explores reproductive stage-dependent responses of rosette leaves to iron availability, revealing distinct growth, elemental contents, and gene expression patterns between young and old leaves and stages.

plant biology↗

bioRxiv2024

Iron homeostasis in the annual and perennial stem zones of Arabis alpina

Plants serve as reservoirs for vital micronutrients, including iron, which they store in bioavailable forms to support growth in subsequent seasons. The perennial life style is preponderant in nature. Annual species allocate iron towards their seeds. However, our understanding of iron homeostasis in perennial plants remains limited. Arabis alpina is a perennial model organism. Its perenniating branches undergo secondary growth where they store carbon-rich macromolecules. In this study, we investigated iron homeostasis in the perennial and annual stem zones (PZ, AZ) of A. alpina. We found that both, the wild-type Pajares (Paj) and perpetual flowering 1 mutant accumulated iron at various developmental stages in the PZ as well as in the AZ. Notably, iron levels in the PZ were found to be approximately two-fold higher than those in the AZ, underscoring the PZs enhanced capacity for iron storage, irrespective of flowering status. Iron was predominantly located within plastid-bound ferritin, providing insight into its storage mechanism. Furthermore, gene expression analyses supported the significance of ferritin and demonstrated an enrichment of transcripts related to iron homeostasis within the stems. Distinct patterns of expression among iron homeostasis genes were observed in relation to iron contents in the PZ and AZ, indicating tissue-specific regulatory mechanisms governing iron accumulation. These findings collectively emphasize the critical function of secondary growth and the PZ as an important site for iron storage in perennial plants, suggesting thatfuture research should further explore the nuances of iron homeostasis signaling in perennial plants. Highlight- Iron accumulates in the perennial stem zone, and ferritin is a storage form for iron there. - Transcripts of iron homeostasis genes are enriched among genes expressed in the annual and perennial stem zones, yet iron accumulation correlates with different gene expression patterns.

plant biology↗

bioRxiv2023

The small iron-deficiency-induced protein OLIVIA and its relation to the bHLH transcription factor POPEYE

Iron (Fe) is a crucial micronutrient needed in many metabolic processes. To balance needs and potential toxicity, plants control the amount of Fe they take up and allocate to leaves and seeds during their development. One important regulator of this process is POPEYE (PYE). PYE is a Fe deficiency-induced key bHLH transcription factor (TF) for allocation of internal Fe in plants. In the absence of PYE, there is altered Fe translocation and plants develop a leaf chlorosis. NICOTIANAMINE SYNTHASE4 (NAS4), FERRIC-REDUCTION OXIDASE3 (FRO3), and ZINC-INDUCED FACILITATOR1 (ZIF1) genes are expressed at higher level in pye-1 indicating that PYE represses these genes. PYE activity is controlled in a yet unknown manner. Here, we show that a small Fe deficiency-induced protein OLIVIA (OLV) can interact with PYE. OLV has a conserved C-terminal motif, that we named TGIYY. Through deletion mapping, we pinpointed that OLV TGIYY and several regions of PYE can be involved in the protein interaction. An OLV overexpressing (OX) mutant line exhibited an enhanced NAS4 gene expression. This was a mild Fe deficiency response phenotype that was related to PYE function. Leaf rosettes of olv mutants remained smaller than those of wild type, indicating that OLV promotes plant growth. Taken together, our study identified a small protein OLV as a candidate that may connect aspects of Fe homeostasis with regulation of leaf growth. HighlightsO_LIOLIVIA (OLV), a small protein, can interact with the bHLH transcription factor POPEYE (PYE) C_LIO_LIOLV has a conserved motif, named TGIYY, that can be involved in protein interaction with PYE C_LIO_LIOLV mutant plants have mild phenotypes related with PYE and NAS4 regulation. C_LIO_LIOLV promotes rosette growth. C_LI

plant biology↗

bioRxiv2023

Constant-pH molecular dynamics simulations of progressive activation in a proton-gated ion channel

Although traditional molecular dynamics simulations successfully capture a variety of different molecular interactions, the protonation states of titratable residues are kept static. A recent constant-pH molecular dynamics implementation in the GROMACS package allows pH effects to be captured dynamically, and promises to provide both the accuracy and computational performance required for studying pH-mediated conformational dynamics in large, complex systems containing hundreds of titratable residues. Here, we demonstrate the applicability of this constant-pH implementation by simulating the proton-gated ion channel GLIC at resting and activating pH, starting from closed and open structures. Our simulations identify residues E26 and E35 as especially pH-sensitive and reveal state-dependent pKa shifts at multiple residues, as well as side chain and domain rearrangements in line with the early stages of gating. Our results are consistent with several previous experimental findings, demonstrating the applicability of constant-pH simulations to elucidate pH-mediated activation mechanisms in multidomain membrane proteins, likely extensible to other complex systems. Significance statementElectrostatic interactions play important roles in protein structure and function. Since changes in pH will (de)protonate residues and thereby modify such interactions, pH itself is a critical environmental parameter. However, protonation states of titratable residues are static during classical molecular dynamics simulations. Recently, a constant-pH algorithm was implemented in the GROMACS package, allowing pH effects to be captured dynamically. Here, we used this implementation to perform constant-pH simulations of the proton-gated ion channel GLIC, providing insight into its activation mechanism by revealing state-dependent shifts in protonation as well as pH-dependent side chain and domain-level rearrangements. The results show that constant-pH simulations are accurate, efficient, and capable of modeling dozens of titratable sites, with important implications for e.g. drug design.

biophysics↗

bioRxiv2023

Characterization of the small Arabidopsis thaliana GTPase and ADP-ribosylation factor-like 2 protein TITAN5

Small GTPases function by conformational switching ability between GDP- and GTP-bound states in rapid cell signaling events. The ADP-ribosylation factor (ARF) family is involved in vesicle trafficking. Though evolutionarily well conserved, little is known about ARF and ARF-like GTPases in plants. Here, we characterized biochemical properties and cellular localization of the essential small ARF-like GTPase TITAN 5/HALLIMASCH/ARL2/ARLC1 (hereafter termed TTN5) from Arabidopsis thaliana. Two TTN5 variants were included in the study with point mutations at conserved residues, suspected to be functional for nucleotide exchange and GTP hydrolysis, TTN5T30N and TTN5Q70L. We found that TTN5 had a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanism. TTN5 acted as a non-classical small GTPase with a remarkably low GTP hydrolysis activity, suggesting it is likely present in GTP-loaded active form in the cell. We analyzed signals from yellow fluorescent protein (YFP)-tagged TTN5 and from in situ immunolocalization of hemagglutine-tagged HA3-TTN5 in Arabidopsis seedlings and in a transient expression system. Together with colocalization using endomembrane markers and pharmacological treatments the microscopic analysis suggests that TTN5 can be present at the plasma membrane and dynamically associated with membranes of vesicles, Golgi stacks and multivesicular bodies. While the TTN5Q70L variant showed similar GTPase activities and localization behavior as wild-type TTN5, the TTN5T30N mutant differed in some aspects. Hence, the unusual capacity of rapid nucleotide exchange activity of TTN5 is linked with cell membrane dynamics, likely associated with vesicle transport pathways in the endomembrane system. HighlightsO_LIThe small ARF-like GTPase TTN5 has a very rapid intrinsic nucleotide exchange capacity with a conserved nucleotide switching mechanism C_LIO_LIBiochemical data classified TTN5 as a non-classical small GTPase, likely present in GTP-loaded active form in the cell C_LIO_LIYFP-TTN5 is dynamically associated with vesicle transport and different processes of the endomembrane system, requiring the active form of TTN5 C_LI

plant biology↗

bioRxiv2023

Small ADP-ribosylation factor-like GTPase TITAN5 (TTN5/ARL2) is linked with the dynamic regulation of IRON-REGULATED TRANSPORTER1

Iron acquisition is crucial for plants. The abundance of IRON-REGULATED TRANSPORTER 1 (IRT1) at the plasma membrane is controlled through endomembrane trafficking. Vesicular trafficking requires small ARF-like GTPases, one of them is TITAN 5 (TTN5). Its physiological functions during the life cycle and cellular targets remain unknown. Little is known how the vesicular trafficking mechanism affects IRT1 localization. We show that TTN5 interacts with the large cytoplasmic variable region and protein-regulatory platform of IRT1. ttn5-1+/- plants have a reduced activity of root iron reductase, needed for iron uptake via IRT1. Fluorescent fusion proteins of TTN5 and IRT1 colocalize at the plasma membrane and in endosomes/multivesicular bodies, where IRT1 sorting and cycling between the plasma membrane and the vacuole are coordinated. Colocalization at the plasma membrane depends partly on the interaction ability of TTN5. TTN5 can also interact with peripheral membrane proteins that are components of the IRT1 regulation machinery, like the trafficking factor SNX1, the C2 domain protein EHB1 and the SEC14-GOLD protein PATL2. Hence, this work links iron acquisition and vesicular trafficking involving a small GTPase of the ARF family. This opens up the possibility to study the involvement of TTN5 in nutritional cell biology in the endomembrane system. HighlightsO_LITTN5 interacts with the large intracellular loop and variable region of IRON-REGULATED TRANSPORTER 1 (IRT1) C_LIO_LITTN5 has a positive effect on root iron (Fe) reductase activity. C_LIO_LITTN5 and IRT1 colocalize at the plasma membrane and in the endomembrane system related to vesicle transport C_LIO_LITTN5 can interact with peripheral membrane proteins of the IRT1 interactome, EHB1, PATL2 and SNX1 suggesting a coordinating role in IRT1 regulation C_LI One-sentence summaryTTN5, a small ARF-like GTPase, is connected to the dynamic regulation of IRON-REGULATED TRANSPORTER 1 (IRT1) in the vesicular trafficking system through direct protein interaction and colocalization, linking with various peripheral membrane proteins of the IRT1 interactome and iron reductase activity.

plant biology↗

bioRxiv2022

FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) accumulates in homo- and heterodimeric complexes in dynamic and inducible nuclear condensates associated with speckle components

Some nuclear proteins undergo condensation, but the functional importance remains often unclear. The basic helix-loop-helix (bHLH) FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) integrates internal and external signals to control iron acquisition and growth. The previously described C-terminal residues Ser271/272 allow FIT to form active complexes with subgroup Ib bHLH factors such as bHLH039. FIT has lower nuclear mobility than mutant FITmSS271AA. Here, we show that FIT undergoes a light-inducible subnuclear partitioning into nuclear condensates that we termed FIT nuclear bodies (NBs). FIT NB characteristics were examined using a standardized FIT NB analysis procedure coupled with different types of quantitative and qualitative microscopy-based approaches. FIT condensates were reversible and likely formed by liquid-liquid phase separation. FIT accumulated preferentially in FIT NBs versus nucleoplasm when engaged in protein complexes with itself and with bHLH039. FITmSS271AA, instead, localized to NBs with different dynamics. FIT colocalized with splicing and light signaling NB markers. The NB-inducing light conditions were linked with active FIT and elevated FIT target gene expression in roots. Hence, we conclude that inducible, highly dynamic FIT condensates form preferentially when transcription factor complexes are active. Inducible FIT nuclear condensates may affect nuclear mobility and integrate environmental and Fe nutrition signals. HighlightsO_LIFIT undergoes light-induced, reversible condensation and localizes to nuclear bodies (NBs), likely via liquid-liquid phase separation C_LIO_LIFunctionally relevant Ser271/272 defines an intrinsically disordered region and influences NB formation dynamics C_LIO_LINBs are preferential sites for FIT dimerization with FIT and bHLH039, dependent on Ser271/272 C_LIO_LIFIT NBs colocalize with NB markers related to splicing and light signaling C_LIO_LILight conditions inducing NBs are linked with active FIT, in agreement with elevated FIT target gene expression in roots C_LI

plant biology↗

bioRxiv2021

The effector FEP3/IRON MAN1 modulates interaction between BRUTUS-LIKE1 and bHLH subgroup IVb and IVc proteins

Plants use the micronutrient iron (Fe) efficiently to balance the requirements for Fe during growth with its potential cytotoxic effects. A cascade of basic helix-loop-helix (bHLH) transcription factors is initiated by bHLH proteins of the subgroups IVb and IVc. This induces more than 50 genes in higher plants that can be grouped in co-expression clusters. Gene co-expression networks contain information on functional protein interactomes. We conducted a targeted yeast two-hybrid screen with pairwise combinations of 23 proteins stemming from previously characterized Fe-deficiency-induced gene co-expression clusters and regulators. We identified novel and described interactions, as well as interaction hubs with multiple interactions within the network. We found that BRUTUS-LIKE E3 ligases (BTSL1, BTSL2) interacted with basic helix-loop-helix (bHLH) transcription factors of the subgroups IVb and IVc including PYE, bHLH104 and ILR3, and with small FE UPTAKE-INDUCING PEPTIDE3/IRON MAN1 (FEP3/IMA1). Through deletion studies and with support of molecular docking, we mapped the interaction sites to three-amino-acid regions in BTSL1 and FEP3/IMA1. The FEP3/IMA1 active residues are present in interacting sites of the bHLH IVc factors. FEP3/IMA1 attenuated interaction of BTSL1 with bHLH proteins in a quantitative yeast three-hybrid assay suggesting that it is an inhibitor. Co-expression of BTSL1 and bHLH IVb and IVc factors uncovered unexpected patterns of subcellular localization. Combining deletion mapping, protein interaction and physiological analysis, we discuss the model that FEP3/IMA1 is a small effector protein inhibiting BTSL1/BTSL2-mediated degradation of bHLH subgroup IVb and IVc proteins. HighlightsO_LIA targeted yeast two-hybrid screen of Fe deficiency-regulated proteins reveals a regulatory protein interactome consisting of E3 ligases BTS/BTSL, bHLH transcription factors of subgroups IVb and IVc and small protein FEP3/IMA1. C_LIO_LIInteraction sites between BTSL1, FEP3/IMA1, and bHLH IVc transcription factors were fine-mapped. C_LIO_LIFEP3/IMA1 is as a small effector protein that selectively attenuates the bHLH interaction with BTSL1 to regulate Fe deficiency responses. C_LI One sentence summaryA targeted protein interaction screen uncovered a interactions of E3 ligase BTSL1, bHLH proteins of subgroup IVb and IVc and effector protein FEP3/IMA1 to regulate Fe deficiency responses.

plant biology↗

bioRxiv2020

Cytokinin-promoted secondary growth and nutrient storage in the perennial stem zone of Arabis alpina

Perennial plants maintain their life span through several growth seasons. Arabis alpina serves as model Brassicaceae species to study perennial traits. A. alpina lateral stems have a proximal vegetative zone with a dormant bud zone, and a distal senescing seed-producing inflorescence zone. We addressed the questions of how this zonation is distinguished at the anatomical level, whether it is related to nutrient storage, and which signals affect the zonation. We found that the vegetative zone exhibits secondary growth, which we termed the perennial growth zone (PZ). High-molecular weight carbon compounds accumulate there in cambium and cambium derivatives. Neither vernalization nor flowering were requirements for secondary growth and sequestration of storage compounds. The inflorescence zone with only primary growth, termed annual growth zone (AZ), or roots exhibited different storage characteristics. Following cytokinin application, cambium activity was enhanced and secondary phloem parenchyma was formed in the PZ and also in the AZ. In transcriptome analysis cytokinin-related genes represented enriched gene ontology terms and were expressed at higher level in PZ than AZ. Thus, A. alpina uses primarily the vegetative PZ for nutrient storage, coupled to cytokinin-promoted secondary growth. This finding lays a foundation for future studies addressing signals for perennial growth. HighlightArabis alpina stems have a perennial zone with secondary growth, where cambium and derivatives store high-molecular weight compounds independent of vernalization. Cytokinins are signals for the perennial secondary growth zone.

plant biology↗

bioRxiv2020

Identifying Behavioral Structure from Deep Variational Embeddings of Animal Motion

AO_SCPLOWBSTRACTC_SCPLOWQuantification and detection of the hierarchical organization of behavior is a major challenge in neuroscience. Recent advances in markerless pose estimation enable the visualization of highdimensional spatiotemporal behavioral dynamics of animal motion. However, robust and reliable technical approaches are needed to uncover underlying structure in these data and to segment behavior into discrete hierarchically organized motifs. Here, we present an unsupervised probabilistic deep learning framework that identifies behavioral structure from deep variational embeddings of animal motion (VAME). By using a mouse model of beta amyloidosis as a use case, we show that VAME not only identifies discrete behavioral motifs, but also captures a hierarchical representation of the motifs usage. The approach allows for the grouping of motifs into communities and the detection of differences in community-specific motif usage of individual mouse cohorts that were undetectable by human visual observation. Thus, we present a novel and robust approach for quantification of animal motion that is applicable to a wide range of experimental setups, models and conditions without requiring supervised or a-priori human interference.

neuroscience↗

bioRxiv2020

Transcriptomic expression patterns of two contrasting lowland rice varieties reveal high iron stress tolerance

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties. Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops. Summary statementLowland rice varieties Hacha and Lachit were selected for contrasting abilities to cope with iron excess stress. Morphological and physiological phenotypes were mirrored by molecular transcriptome changes, indicating altered metal homeostasis in the root as an adaptive tolerance mechanism in Lachit.

plant biology↗