Biology subjects

Ibrahim, T.

Publications and source records attributed to Ibrahim, T..

11 recordsLinked to original sources

bioRxiv2026

Mitochondrial dysfunction as a hallmark of brain senescence in telomerase-deficient mice

Neurodegenerative diseases, including Alzheimer's disease (AD), are strongly associated with aging. However, the molecular mechanisms underlying pathological brain aging remain incompletely understood. In this study, we used a mouse model of telomere attrition, a major driver of cellular senescence, to perform an unbiased analysis of how telomere-driven senescence affects cellular physiology and contributes to processes relevant to neurodegenerative conditions. After validating the presence of senescence hallmarks in telomerase-deficient brains, we characterized their transcriptomic and proteomic profiles. Mitochondrial function and associated energy metabolism emerged as the major dysregulated pathways, driven predominantly by proteomic rather than transcriptomic changes. Functional biochemical analyses on isolated brain mitochondria demonstrated impaired electron transport chain (ETC) complex activity and reduced energetic status, despite preserved ETC complex integrity and mitochondrial content. Further analyses in senescent primary neurons indicated an accumulation of dysfunctional mitochondria, characterized by increased reactive oxygen species (ROS) production and reduced ATP levels, although basal cellular respiration was maintained. At the tissue level, these alterations were associated with moderate reductions in neuronal density in the subiculum and cortical layer V, indicating region-specific vulnerability rather than widespread neurodegeneration. We propose that a major consequence of telomere dysfunction associated with pathological brain aging is the downregulation of mitochondrial activity, which contributes to the selective vulnerability of specific brain regions. These findings highlight mitochondrial pathways as attractive targets for interventions aimed at preserving brain health during aging.

neuroscience↗

bioRxiv2026

A broad-host-range Rhizobium rhizogenes strain enables transient expression across diverse crops and establishes functional assays in faba bean

Agrobacterium-mediated transient expression has revolutionized plant research, enabling numerous landmark discoveries across diverse areas of plant biology. Yet this powerful approach remains largely confined to solanaceous species, leaving most economically important crop families without a comparable rapid assay platform. Here, we show that an engineered Rhizobium rhizogenes strain, AS109, mediates efficient transient expression across diverse dicot species spanning multiple taxonomic families, consistently outperforming commonly used laboratory agrobacterial strains. Leveraging the broad host range of AS109, we establish a suite of functional assays in faba bean (Vicia faba), including protein localisation, RNA interference-mediated gene silencing, cell-surface elicitor recognition screens, nucleotide-binding leucine-rich repeat receptor (NLR) activation, and infection cell biology at the host-pathogen interface. We further demonstrate that both singleton NLRs and sensor-helper NLR pairs from Solanaceae retain effector recognition and cell death activity when transferred into faba bean, establishing a rapid platform for evaluating cross-family transferability of disease-resistance genes. AS109 thus provides an accessible and versatile chassis for functional genomics in non-model crops, bridging the widening gap between hypothesis generation and experimental validation across diverse plant species.

plant biology↗

bioRxiv2026

View Tomo: Context-aware targeting and analysis in electron cryo-tomography

Electron cryo-tomography (cryoET) resolves cellular structure in three dimensions, yet region selection is still typically based on two-dimensional projection images. Here, we introduce View Tomo, a workflow for rapid acquisition of low-magnification tomograms that enables screening, targeting and analysis in 3D. View Tomo tilt series are acquired in minutes at low dose (~3 e-/[A]2), producing high-contrast tomograms that remain compatible with subsequent high-resolution structural determination. We implemented View Tomo using an automated acquisition and reconstruction pipeline for rapid alignment. Across multiple viral and cellular systems, view tomograms revealed membrane remodelling events, assembly intermediates and cellular organisation that are difficult to identify in projection images. These data enabled targeted high-resolution imaging and quantitative analysis of spatial relationships within cells. View Tomo therefore extends cryoET workflows by improving target selection, enabling analysis of mesoscale organisation, and facilitating integration with correlative imaging approaches.

cell biology↗

bioRxiv2025

A dual component system instructs membrane hydrolysis during the final stages of plant autophagy

Autophagy is an intracellular catabolic process conserved across eukaryotes and critical for plant stress tolerance. Upon their delivery in the vacuole, how autophagic bodies containing cargo are hydrolyzed to warrant autophagy degradation remains poorly characterized. Here, we identify two Arabidopsis phospholipases as core components of the autophagy machinery. We find that LCAT3 and LCAT4 traffic to the vacuolar lumen and converge on autophagic bodies using differential pathways, placing them on the outer and inner side of the vesicle, respectively. Double knockouts lcat3,4 accumulate autophagic bodies and show reduced autophagy activity. In vivo reconstitution demonstrates that LCAT3 can hydrolyze the membrane of autophagic bodies, enabling the activity of LCAT4 to enhance this process. In sum, our work reveals that the concerted action of a multi-component system is required for the efficient and specific disruption of autophagic bodies as an obligatory step for the completion of the autophagy pathway.

plant biology↗

bioRxiv2024

Truncated TrkB: The predominant TrkB Isoform in Nociceptors

Truncated TrkB (TrkBT1), traditionally considered a dominant-negative regulator of full-length TrkB (TrkBTK+), remains poorly understood in peripheral sensory neurons, particularly nociceptors. Furthermore, sensory neuronal TrkB expression and function has been traditionally associated with non-nociceptive neurons, particularly A{delta} low-threshold mechanoreceptors. This study challenges prevailing assumptions by demonstrating that TrkBT1 is the predominant TrkB isoform expressed in sensory neurons and plays a functional role in modulating neuronal activity. We demonstrate that TrkBT1 is the predominant isoform expressed in nociceptors, identified by markers such as TRPV1, TRPA1, TRPM8 and 5HT3A, as well as non-nociceptors, while the full-length isoform (TrkBTK+) is restricted to non-nociceptive subpopulation. Functionally, we show that acute application of BDNF induces modest calcium influx in nociceptors and prolonged BDNF exposure significantly potentiates capsaicin-induced calcium influx, an effect blocked by the TrkB-specific antagonist ANA12. Additionally, BDNF also promotes the survival of both nociceptive and non-nociceptive neurons in culture, an effect dependent on TrkBT1 activity. Our data also reveal that ANA12 inhibits BDNF-mediated neuronal sensitization and survival in a concentration-dependent manner, implicating distinct TrkBT1 signaling pathways in these processes. Collectively, our findings redefine TrkBT1 as a functional modulator of nociceptor activity rather than a passive regulator of full-length TrkB. By uncovering its dual roles in nociceptor sensitization and survival, this study provides new insights into the molecular mechanisms of BDNF/TrkB signaling in pain. Future work evaluating the role of TrkBT1 in sensory biology could offer new perspectives on how this receptor contributes to neuronal function and plasticity during chronic pain conditions.

neuroscience↗

bioRxiv2024

A helper NLR targets organellar membranes to trigger immunity

Upon activation, plant NLR immune receptors are known to assemble into oligomeric resistosomes that insert into the plasma membrane, forming Ca2+-permeable channels and triggering immunity. Here, we show that the RPW8-like coiled-coil (CCR-) NLR NRG1 primarily targets organelles instead of the plasma membrane. Unlike canonical CC-NLRs, activated NRG1 accumulates at the chloroplast envelope and channels stromal Ca2+ into the cytosol. AlphaFold modeling of the NRG1 resistosome reveals an unusually long N-terminal membrane-insertion structure that would span the double chloroplast membranes. Nanobody-mediated relocalization shows functional membrane specificity: chloroplast trapping abolishes activity of the canonical helper CC-NLR NRC4 but not NRG1. NRG1 orthologs, from non-flowering lineages to angiosperms, target chloroplasts, suggesting that organelle-centered defense dates back to at least [~]360 million years. We propose that coiled-coil NLR diversification has enabled compartment-specific immune signaling to capture diverse Ca2+ stores.

plant biology↗

bioRxiv2024

An oomycete effector co-opts a host RabGAP protein to remodel pathogen interface and subvert defense-related secretion

Pathogens have evolved sophisticated mechanisms to manipulate host cell membrane dynamics, a crucial adaptation to survive in hostile environments shaped by innate immune responses. Plant- derived membrane interfaces, engulfing invasive hyphal projections of fungal and oomycete pathogens, are prominent junctures dictating infection outcomes. Understanding how pathogens transform these host-pathogen interfaces to their advantage remains a key biological question. Here, we identified a conserved effector, secreted by plant pathogenic oomycetes, that co-opts a host Rab GTPase-activating protein (RabGAP), TBC1D15L, to remodel the host-pathogen interface. The effector, PiE354, hijacks TBC1D15L as a susceptibility factor to usurp its GAP activity on Rab8a--a key Rab GTPase crucial for defense-related secretion. By hijacking TBC1D15L, PiE354 purges Rab8a from the plasma membrane, diverting Rab8a-mediated immune trafficking away from the pathogen interface. This mechanism signifies an uncanny evolutionary adaptation of a pathogen effector in co- opting a host regulatory component to subvert defense-related secretion, thereby providing unprecedented mechanistic insights into the reprogramming of host membrane dynamics by pathogens.

plant biology↗

bioRxiv2023

Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins can engage in complex interactions to detect pathogens and execute a robust immune response via downstream helper NLRs. However, the biochemical mechanisms of helper NLR activation by upstream sensor NLRs remain poorly understood. Here, we show that the coiled-coil helper NLR NRC2 accumulates in vivo as a homodimer that converts into a higher order oligomer upon activation by its upstream virus disease resistance protein Rx. The Cryo-EM structure of NRC2 in its resting state revealed intermolecular interactions that mediate homodimer formation. These dimerization interfaces have diverged between paralogous NRC proteins to insulate critical network nodes and enable redundant immune pathways. Our results expand the molecular mechanisms of NLR activation pointing to transition from homodimers to higher-order oligomeric resistosomes.

plant biology↗

bioRxiv2023

Sex-dependent Differences in the Genomic Profile of Lingual Sensory Neurons in Naive and Tongue-Tumor Bearing Mice

Mechanisms of sex-dependent orofacial pain are widely understudied. A significant gap in knowledge exists about comprehensive regulation of tissue-specific trigeminal sensory neurons in diseased state of both sexes. Using RNA sequencing of FACS sorted retro-labeled sensory neurons innervating tongue tissue, we determined changes in transcriptomic profiles in males and female mice under naive as well as tongue-tumor bearing conditions Our data revealed the following interesting findings: 1) Tongue tissue of female mice was innervated with higher number of trigeminal neurons compared to males; 2) Naive female neurons innervating the tongue exclusively expressed immune cell markers such as Csf1R, C1qa and others, that werent expressed in males. This was validated by Immunohistochemistry. 4) Accordingly, immune cell markers such as Csf1 exclusively sensitized TRPV1 responses in female TG neurons. 3) Male neurons were more tightly regulated than female neurons upon tumor growth and very few differentially expressed genes (DEGs) overlapped between the sexes, 5) Male DEGs contained higher number of transcription factors whereas female DEGs contained higher number of enzymes, cytokines and chemokines. Collectively, this is the first study to characterize the effect of sex as well as of tongue-tumor on global gene expression, pathways and molecular function of tongue-innervating sensory neurons.

neuroscience↗

bioRxiv2022

Telomere-induced senescence increases aberrant intraneuronal amyloid-β accumulation by impairing autophagy in a mouse model of Alzheimer's disease

Aging is a well-known risk factor for Alzheimers disease (AD) and other neurodegenerative pathologies, but the molecular and cellular changes occurring in the aging brain are poorly understood. AD pathology seems to correlate with the appearance of cells that become senescent due to the progressive accumulation of cellular insults causing DNA damage. In this study, we investigated the role of cellular senescence on AD pathology by crossing an amyloid-{beta} (A{beta}) mouse model of AD (5xFAD) with a mouse model of senescence that is genetically deficient for the RNA component of the telomerase (Terc-/-). Our results show that accelerated senescence reduces amyloid plaque formation and A{beta} levels at an age when full-blown amyloid pathology is observed in 5xFAD mice. However, early and aberrant intraneuronal A{beta} accumulation is observed in the subiculum and cortical layer V of senescent mice. Selective neurodegeneration linked to telomere attrition and early intraneuronal A{beta} accumulation was observed in these particular regions. Finally, our results suggest that the effect of senescence on amyloid pathology might be mediated through an alteration in autophagy function. Altogether, these findings demonstrate the instrumental role of senescence in intraneuronal A{beta} accumulation associated to AD pathophysiology, and further support future approaches targeting these processes for therapeutic intervention.

neuroscience↗

bioRxiv2022

AF2-multimer guided high accuracy prediction of typical and atypical ATG8 binding motifs

Macroautophagy/autophagy is an intracellular degradation process central to cellular homeostasis and defense against pathogens in eukaryotic cells. Regulation of autophagy relies on hierarchical binding of autophagy cargo receptors and adaptors to ATG8/LC3 protein family members. Interactions with ATG8/LC3 are typically facilitated by a conserved, short linear sequence, referred to as the ATG8/LC3 interacting motif/region (AIM/LIR), present in autophagy adaptors and receptors as well as pathogen virulence factors targeting host autophagy machinery. Since the canonical AIM/LIR sequence can be found in many proteins, identifying functional AIM/LIR motifs has proven challenging. Here we show that protein modelling using Alphafold-Multimer (AF2-multimer) identifies both canonical and atypical AIM/LIR motifs with a high level of accuracy. AF2-multimer can be modified to detect additional functional AIM/LIR motifs by using protein sequences with mutations in primary AIM/LIR residues. By combining protein modelling data from AF2-multimer with phylogenetic analysis of protein sequences and protein-protein interaction assays, we demonstrate that AF2-multimer predicts the physiologically relevant AIM motif in the ATG8-interacting protein 2 (ATI-2) as well as the previously uncharacterized non-canonical AIM motif in ATG3 from potato (Solanum tuberosum). AF2-multimer also identified the AIM/LIR motifs in pathogen-encoded virulence factors that target ATG8 members in their plant and human hosts, revealing that cross-kingdom ATG8-LIR/AIM associations can also be predicted by AF2-multimer. We conclude that the AF2-guided discovery of autophagy adaptors/receptors will substantially accelerate our understanding of the molecular basis of autophagy in all biological kingdoms.

molecular biology↗