Biology subjects

Grujic, N.

Publications and source records attributed to Grujic, N..

17 recordsLinked to original sources

bioRxiv2026

Rules of disengagement: orexin-arousal and dopamine-utility as separable axes

Staying on task, leaving it, and coming back to it are processes we experience daily. They depend on task utility and arousal, but the neurochemical processes behind this interplay are unknown. In mice performing a decision-making task with shifting reward size, we identified latent engagement states and the transitions between them. Pupil-linked arousal and dopaminergic utility coding predicted these transitions along separable axes. Orexin antagonism with almorexant disengaged mice at low reward, an effect mediated by pupil-linked arousal and not by dopamine. GLP-1 receptor agonism with semaglutide reduced the gain with which accumbal dopamine integrates reward history, which predicted the progressive disengagement it caused, with no detectable contribution from arousal or orexin. Fast striatal and slow accumbal dopamine codes predicted engagement on their own timescales. These results decouple orexin-driven arousal from dopamine-mediated utility coding in task engagement, with implications for two widely used drug classes and for disorders of motivation.

neuroscience↗

bioRxiv2026

CAN1-mediated autophagosome size regulation fine-tunes phosphate starvation tolerance in Arabidopsis thaliana

Inorganic phosphate (Pi) availability determines root development and plant performance. In Arabidopsis thaliana, external Pi is sensed by root tips and Pi limitation triggers ER stress-induced autophagy, yet the physiological impact and mechanisms controlling autophagosome biogenesis remain unclear. Here, we identify CANE1 (COMPONENT OF AUTOPHAGIC NETWORK) as a novel plant-specific regulator of autophagosome size in local Pi sensing. CANE1 associates with the plasma membrane-ER tethering protein VAP27-1 and binds to Pi-responsive ATG8 isoforms through conserved interaction motifs. Loss of CANE1 augments ER stress resistance by reducing autophagosome size in Pi-deprived root tips. Our findings establish CANE1 as a determinant of autophagosome size at the ER membrane. Thus, CANE1 functions as a molecular link between Pi-dependent ER stress signaling and fine-tuning of autophagic capacity.

plant biology↗

bioRxiv2025

Ancestral P-body proteins rewired for autophagic recyclingin the early land plant Marchantia polymorpha

Processing bodies (P-bodies) are conserved ribonucleoprotein (RNP) granules central to RNA metabolism across eukaryotes. Although the mechanisms underlying their assembly are well understood, the pathways governing their selective turnover remain unclear. Here, we identify the conserved decapping proteins EDC4 and DCP1 as a selective autophagy receptor pair responsible for P-body turnover in the early land plant Marchantia polymorpha. MpEDC4 engages ATG8 via a canonical AIM motif, while MpDCP1 contains a previously unrecognized reverse AIM within its intrinsically disordered region. Mutations disrupting these motifs impair autophagic degradation of P-bodies, demonstrating a cooperative receptor mechanism. Notably, this autophagic function is lineage-specific, as orthologs in Arabidopsis and humans lack ATG8-binding capacity. Strikingly, heterologous expression of MpEDC4 in human cells promotes degradation of -synuclein, a protein strongly linked to Parkinsons disease etiology. Our findings thus uncover an evolutionary innovation that links RNA metabolism to selective autophagy and opens avenues for cross-kingdom engineering of targeted protein degradation pathways.

plant biology↗

bioRxiv2025

Neurometabolic signaling and control of policy complexity

Cognition and adaptive behavior emerge from neural information processing. This must operate within finite metabolic constraints, since neural information processing is metabolically expensive. While neural implementations of action selection and learning are well-studied, systems allocating the informational capacity required to encode complex behavioral policies remain unknown. We hypothesized that hypothalamic hypocretin/orexin neurons (HONs) are uniquely positioned to signal and control policy complexity, given that they are activated by metabolic depletion and influence decision-making systems. To explore this, we employed a set of cell/neurotransmitter-specific imaging and causal manipulations during a multi-armed bandit task where freely behaving mice learned probabilistic state-action-reward relationships (together [~]100,000 decisions from >100 mice). Miniscope recordings of HON activity revealed that pre-choice, but not post-choice activity correlates with decision policy, dissociating decisions from feedback. Furthermore, manipulating HON signals with optogenetics and pharmacology confirmed that they causally regulate the development of complex policies. Finally, neurotransmitter-specific sensors revealed that hypocretin/orexin receptors modulate decision policy-related dopamine and noradrenaline dynamics in the nucleus accumbens and medial prefrontal cortex. These findings identify HONs as subcortical regulators of policy complexity, encoding critical signals for decision-making adjustments. This opens a new window for the development of comprehensive mechanistic models of strategic learning which account for interplay between decision-making policies and metabolic/informational constraints, and may guide the development of potential treatments for disorders with policy deficits such as autism and schizophrenia.

neuroscience↗

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

Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants

Selective autophagy is a fundamental protein quality control pathway that safeguards proteostasis by degrading damaged or surplus cellular components, particularly under stress. This process is orchestrated by selective autophagy receptors (SARs) that direct specific cargo for degradation. While significant strides have been made in understanding the molecular framework of selective autophagy, the diversity of SAR repertoires across species remain largely unexplored. Through a comparative interactome analysis across five model organisms, we identified a suite of conserved and lineage-specific SAR candidates. Among these, we validated CESAR as a conserved SAR critical for proteostasis under heat stress. CESAR specifically facilitates the degradation of hydrophobic, ubiquitinated protein aggregates and is indispensable for heat stress tolerance. Our study offers a rich resource for SAR discovery and positions CESAR as a pivotal regulator of proteostasis, with broad implications for improving stress resilience in plants.

plant biology↗

bioRxiv2024

Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape

The evolution of cellular complexity hinges on the capacity of multimeric protein complexes to diversify without compromising their ancestral functions. A central question is how individual subunits within these complexes can evolve novel functions while maintaining the integrity of the original assembly. Here, we explore this question by tracing the evolutionary trajectory of the plant exocyst, an octameric complex essential for exocytosis in eukaryotes. Remarkably, the Exo70 subunit underwent dramatic expansion and functional divergence in plants. We demonstrate that electrostatic alterations in the N-terminal region of the Exo70 subunit precipitated its dissociation from the exocyst complex. This release mitigated paralog interference, thereby facilitating the subunits extensive functional co-option. Our findings reveal a nuanced mechanism by which a protein subunit, ancestrally constrained within a multimeric complex, can escape those constraints and evolve novel functions, shedding light on the molecular underpinnings of cellular innovation. One-Sentence SummaryEvolutionary diversification of an exocyst subunit is driven by electrostatic shifts that dissociates it from the ancestral complex.

evolutionary biology↗

bioRxiv2024

Distinct bandwidths of orexin neuron activity independently encode body movement and metabolic state

Tracking net body movement in real time may enable the brain to estimate ongoing demands and thus better orchestrate muscle tone, energy balance, and arousal. To identify neural populations specializing in tracking net body movement, here we compared self-initiated movement-related activity across genetically-defined subcortical neurons in the mouse brain, including dopaminergic, glutamatergic, noradrenergic, and key peptidergic neurons. We show that hypothalamic orexin/hypocretin-producing neurons (HONs) are exceptionally precise movement-trackers, encoding net body movement across multiple classified behaviors with a high degree of precision, independent of head acceleration. This tracking was so precise, that video analysis of the mouse body movement reliably served as a low-cost biometric for HON population activity. The movement tracking was independent of internal nutritional states, and occurred in a communication bandwidth distinct from HON encoding of blood glucose. At key projection targets, orexin/hypocretin peptide outputs correlated with self-initiated movement in a projection-specific manner, indicating functional heterogeneity in HON outputs. Finally, we found that body movement was not encoded to the same extent in other key neural populations related to arousal or energy. These findings indicate that subcortical orchestrators of arousal and metabolism are finely tuned to encode net body movement, constituting a bridge multiplexing ongoing motor activity with internal energy resources.

neuroscience↗

bioRxiv2024

Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage

AbstractRNA viruses co-opt the host endomembrane system and organelles to build replication complexes for infection. How the host responds to these membrane perturbations is poorly understood. Here, we explore the autophagic response of Arabidopsis thaliana to three viruses that hijack different cellular compartments. Autophagy is significantly induced within systemically infected tissues, its disruption rendering plants highly sensitive to infection. Contrary to being an antiviral defense mechanism as previously suggested, quantitative analyses of the viral loads established autophagy as a tolerance pathway. Further analysis of one of these viruses, the Turnip Crinkle Virus (TCV) that hijack mitochondria, showed that despite perturbing mitochondrial integrity, TCV does not trigger a typical mitophagy response. Instead, TCV and Turnip yellow mosaic virus (TYMV) infection activates a distinct selective autophagy mechanism, where oligomeric metabolic enzymes moonlight as selective autophagy receptors and degrade key executors of defense and cell death such as EDS1. Altogether, our study reveals an autophagy-regulated metabolic rheostat that gauges cellular integrity during viral infection and degrades cell death executors to avoid catastrophic amplification of immune signaling.

plant biology↗

bioRxiv2024

ATG8ylation of vacuolar membrane protects plants against cell wall damage

Vacuoles are essential for cellular metabolism, growth, and the maintenance of internal turgor pressure. They sequester lytic enzymes, ions, and secondary metabolites that, if leaked into the cytosol, could lead to cell death. Despite their pivotal roles, quality control pathways that safeguard vacuolar integrity remained elusive in plants. Here, we discovered a conserved vacuolar quality control (VQC) pathway that is activated upon cell wall damage in a turgor pressure dependent manner. Cell wall perturbations induce a distinct modification - ATG8ylation - on the vacuolar membrane (tonoplast) that is regulated by the V-ATPase and ATG8 conjugation machinery. Genetic disruption of tonoplast ATG8ylation impairs vacuolar integrity, leading to cell death. Together, our findings reveal a homeostatic pathway that preserves vacuolar integrity upon cell wall damage.

plant biology↗

bioRxiv2023

Exploratory rearing is governed by hypothalamic MCH cells according to the locus coeruleus

Exploration is essential for survival because it allows animals to gather information about their environment. Rearing is a classic exploratory behavior, during which an animal transiently stands on its hind legs to sample its environment. It is widely observed in common lab conditions as well as in the wild, yet neural signals and circuits underlying this fundamental component of innate behavior remain unclear. We examined behavioral correlates of activity in hypothalamic MCH-producing neurons (MNs) - a recently characterized but still poorly understood neural type - and found that MN activation co-occurs with exploratory rears in mice. Complementary optogenetic and pharmacological manipulations indicated that MN activity selectively promotes rearing via G-protein coupled MCHR1 receptors. Furthermore, we show in vivo that activation of the locus coeruleus noradrenergic neurons rapidly inhibits MNs and suppresses rearing through MCHR1-dependent pathways. Overall, these findings define a subcortical neural module which both tracks and controls exploratory rearing.

neuroscience↗

bioRxiv2022

Shuffled ATG8 interacting motifs form an ancestral bridge between UFMylation and C53-mediated autophagy

UFMylation mediates the covalent modification of substrate proteins with UFM1 (Ubiquitin-fold modifier 1) and regulates the selective degradation of endoplasmic reticulum (ER) via autophagy (ER-phagy) to maintain ER homeostasis. Specifically, collisions of the ER-bound ribosomes trigger ribosome UFMylation, which in turn activates C53-mediated autophagy that clears the toxic incomplete polypeptides. C53 has evolved non-canonical shuffled ATG8 interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. Why these non-canonical motifs were selected during evolution, instead of canonical ATG8 interacting motifs remains unknown. Here, using a phylogenomics approach, we show that UFMylation is conserved across the eukaryotes and secondarily lost in fungi and some other species. Further biochemical assays have confirmed those results and showed that the unicellular algae, Chlamydomonas reinhardtii has a functional UFMylation machinery, overturning the assumption that this process is linked to multicellularity. Our conservation analysis also revealed that UFM1 co-evolves with the sAIMs in C53, reflecting a functional link between UFM1 and the sAIMs. Using biochemical and structural approaches, we confirmed the interaction of UFM1 with the C53 sAIMs and found that UFM1 and ATG8 bound to the sAIMs in a different mode. Conversion of sAIMs into canonical AIMs prevented binding of UFM1 to C53, while strengthening ATG8 interaction. This led to the autoactivation of the C53 pathway and sensitized Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral toggle switch embodied in the sAIMs that regulates C53-mediated autophagy to maintain ER homeostasis.

plant biology↗

bioRxiv2022

Coding of reward uncertainty and probability by orexin neurons

Activation of hypothalamic hypocretin/orexin neurons (HONs) is a neural substrate of arousal. HONs activate during sensory stimuli, and are thus thought to regulate arousal according to sensory input. Here, we measured body movements occurring during sound cues or associated reward outcomes, and used an encoding model to ask whether HONs indeed specialize in tracking certain features, or multiplex diverse types of features. Although some single HONs multiplexed feature combinations, during the cue period the overall HON signal primarily tracked body movements. This persisted across cues signaling different reward probabilities, and substantially diverged from reward-probability tracking in concurrently-recorded VTA dopamine neurons. In contrast, during reward outcome, HONs predominantly signaled the presence or absence of reward, and not body movements, nor surprise or reward prediction error. These results describe an unexpectedly specialized and flexible logic of HON activation, suggesting a role for HONs in tracking actions and subsequent reinforcements.

neuroscience↗

bioRxiv2022

Control and coding of pupil size by hypothalamic orexin neurons

Brain orexin (hypocretin) neurons are implicated in sleep-wake switching and reward-seeking, but their roles in rapid arousal dynamics and reward perception remain unclear. Here, cellspecific stimulation, deletion, and in vivo recordings revealed strong correlative and causal links between pupil dilation - a quantitative arousal marker - and orexin cell activity. Coding of arousal and reward was distributed across orexin cells, indicating that they specialize in rapid, multiplexed communication of momentary arousal and reward states.

neuroscience↗

bioRxiv2021

Rational inattention in mice

Behavior exhibited by humans and other organisms is generally inconsistent and biased, and thus is often labeled irrational. However, the origins of this seemingly suboptimal behavior remain elusive. We developed a behavioral task and normative framework to reveal how organisms should allocate their limited processing resources such that there is an advantage to being imprecise and biased for a given metabolic investment that guarantees maximal utility. We found that mice act as rational-inattentive agents by adaptively allocating their sensory resources in a way that maximizes reward consumption in novel stimulus-reward association environments. Surprisingly, perception to commonly occurring stimuli was relatively imprecise, however this apparent statistical fallacy implies "awareness" and efficient adaptation to their neurocognitive limitations. Interestingly, distributional reinforcement learning mechanisms efficiently regulate sensory precision via top-down normalization. These findings establish a neurobehavioral foundation for how organisms efficiently perceive and adapt to environmental states of the world within the constraints imposed by neurobiology.

neuroscience↗

bioRxiv2019

The Pleiades cluster of fungal effector genes inhibit 1 host defenses

SummaryBiotrophic plant pathogens secrete effector proteins to manipulate the host physiology. Effectors suppress defenses and induce an environment favorable to disease development. Sequence-based prediction of effector function is difficulted by their rapid evolution rate. In the maize pathogen Ustilago maydis, effector-coding genes frequently organize in clusters. Here we describe the functional characterization of the pleiades, a cluster of ten symplastic effectors. Deletion of the pleiades leads to strongly impaired virulence and accumulation of reactive oxygen species (ROS) in infected tissue. Eight of the Pleiades suppress the production of ROS upon perception of pathogen associated molecular patterns (PAMPs). Although genetically redundant, the Pleiades target different host components. The paralogs Taygeta1 and Merope1 suppress ROS production in either the cytoplasm or nucleus, respectively. Merope1 targets and promotes the autoubiquitination activity of RFI2, a conserved family of E3 ligases that regulates the production of PAMP-triggered ROS burst and influences flowering time in plants.

microbiology↗

bioRxiv2018

Peri-saccadic perceptual mislocalization is different for upward saccades

Saccadic eye movements, which dramatically alter retinal images, are associated with robust peri-movement perceptual alterations. Such alterations, thought to reflect brain mechanisms for maintaining perceptual stability in the face of saccade-induced retinalimage disruptions, are often studied by asking subjects to localize brief stimuli presented around the time of horizontal saccades. However, other saccade directions are not usually explored. Motivated by recently discovered asymmetries in upper and lower visual field representations in the superior colliculus, a structure important for both saccade generation and visual analysis, here we observed significant differences in peri-saccadic perceptual alterations for upward saccades relative to other saccade directions. We also found that, even for purely horizontal saccades, perceptual alterations differ for upper versus lower retinotopic stimulus locations. Our results, coupled with conceptual modeling, suggest that peri-saccadic perceptual alterations might critically depend on neural circuits, like superior colliculus, that asymmetrically represent the upper and lower visual fields.

neuroscience↗