Biology subjects

Ranjan, A.

Publications and source records attributed to Ranjan, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Disentangling blade and vasculature shape in grapevine leaves

The leaf blade and vasculature develop together within a shared morphological space. Despite shared molecular patterning pathways, it is unknown if developmental and evolutionary variation affect these tissues separately or together in a coordinated way. Grapevine leaves have a morphometric history and abundant data measuring the shape of the blade and vasculature together. Using a combination of topological data analysis and deep learning, we perform reciprocal semantic segmentation of leaf blade and vasculature. Each tissue contains sufficient information to predict the other. We hypothesize that this is due to a one-to-one relationship between blade and vein. Using thin plate splines to swap and warp different combinations of blade and vein shapes, we show that a set of leaves with a many-to-one relationship of blade and vein are distinguishable from true leaves. We also swap blade and vein across the developmental series and between species and show that only reversing the developmental series disrupts the relationship between blade and vasculature. We end by discussing the evolutionary and developmental implications that there is a unique, one-to-one mapping between blade and vein that allows each to be predicted from the other. Author summaryLeaves are made of two closely connected parts: the flat blade that captures light and the network of veins that transports water, nutrients, and developmental signals. Although these tissues grow together and share common molecular patterning pathways, it has remained unclear whether a particular blade shape is uniquely linked to a specific vein pattern. In this study, we use grapevine leaves as a model system and combine mathematical shape analysis with deep learning to examine this relationship. We show that the shape of the blade alone can accurately predict the vein network, and that the vein network can likewise predict the blade. This finding suggests a near one-to-one relationship between these two tissues. To test this idea, we created artificial leaves in which blade and vein shapes were deliberately mismatched. Although these synthetic leaves appeared realistic at a global level, a neural network was able to distinguish them from real leaves based on subtle differences. We further show that this tight coupling is maintained by the developmental sequence of leaf growth rather than by species identity, revealing a conserved constraint linking leaf form and internal structure.

plant biology↗

bioRxiv2026

KAMALA, a genome edited rice variety with improved yield by finetuning cytokinin oxidase activity released in India

Increasing yield is of major importance for Asian and African food security. Knock out mutants in the rice cytokinin oxidase gene CKX2 had shown potential for yield improvement. Here we explored whether subtle changes in CKX2 activity by editing FAD and cytokinin binding site sequences could improve the Indian mega-variety Samba Mahsuri. Knock out and single mutants in FAD and cytokinin binding sites induced by CRISPR/Cas12a caused moderate yield increases. Among 80 CKX2 alleles, five lines with in-frame mutations in both FAD and cytokinin binding domains produced even higher yield. One line, KAMALA, showed superior agronomic performance in 18 field locations (irrigated and rainfed ecologies) over three seasons in trials conducted by AICRPR (All India Coordinated Research Project on Rice), with an average 19% grain yield increase, early maturity, complete panicle emergence, and unaltered grain quality. KAMALA was registered as the first genome-edited variety ready for cultivation by Indian farmers.

plant biology↗

bioRxiv2026

Leveraging HIV-Specific CAR T Cells and Rapamycin Treatment in Kick-and-Kill HIV Cure Approaches

HIV is not cured with currently available combination antiretroviral therapy (ART) alone in large part because the virus establishes virologic latency in long lived CD4+ cells. To eliminate this latent reservoir, as required for HIV eradication, latency reversing agents (LRAs) are being developed to force HIV out of latency and induce infected cells to express viral proteins leading to their clearance, in a so-called "Kick-and-Kill" approach. This strategy relies on the immune system to clear the productively-infected cells and is thus limited by HIV immune evasion and the immunological exhaustion that occurs during HIV infection. To counter these limitations and augment an LRA-mediated HIV cure approach, we report herein the utility of HIV-specific truncated CD4-based D1D2 CAR T cells combined with LRA treatment and the mTORC1 inhibitor rapamycin to reduce immune exhaustion and specifically target and kill LRA-stimulated HIV infected cells. We demonstrate that rapamycin does not prevent HIV latency reversal via multiple classes of LRAs in several in vitro models, suggesting that it is compatible with cure approaches utilizing these LRAs. Additionally, rapamycin does not inhibit the early T cell activation (CD69 upregulation) in primary T cells that occurs during protein kinase C (PKC) modulator-mediated HIV latency reversal. Furthermore, in vitro chronically exhausted CAR T cells were found to have a higher frequency of terminally exhausted PD-1+Tim-3+ and CD69+PD-1+ cells when compared to CAR T cells that were cultured under the same conditions in the presence of rapamycin, validating the use of the mTORC1 inhibitor rapamycin to prevent immune exhaustion of CAR T cells. Finally, we found that latently-infected cells that were stimulated to express HIV proteins using a designed, synthetic PKC modulator LRA (SUW133) were efficiently recognized and killed by CAR T cells. Overall, these data demonstrate the compatibility of immune rejuvenation using rapamycin with HIV reservoir depletion using LRAs and CAR T cells. This combination therapy strategy represents a promising approach to more effectively target the latent reservoir in HIV cure approaches.

immunology↗

bioRxiv2025

A cytokinin-auxin antagonistic module regulates nitrogen-triggered tiller outgrowth in rice

Tillering is a key trait that shapes aboveground architecture and directly contributes to rice yield. However, integration of environmental cues to genetic regulators for controlling tiller outgrowth remains poorly understood. We investigated the effects of nitrogen, one of the critical environmental factors, on the early stages of tiller bud outgrowth. Comprehensive temporal transcriptomic analyses in response to two nitrogen forms, nitrate (NO -) and ammonium (NH +), identified gene-regulatory networks for nitrogen-triggered tiller outgrowth, with phytohormone signaling as the central interface. Pharmacological, molecular, and genetic experiments established cytokinin-auxin antagonism as a central regulator of the nitrogen-mediated tillering. Cytokinin promoted bud outgrowth by repressing the TCP transcription factor OsTB1, the key inhibitor of tillering, via Cytokinin Response Factors OsERF53/54. OsERF53/54 further reduced polar auxin transport by repressing OsPIN1a to promote bud activation. Conversely, auxin promoted bud dormancy by inducing OsTB1 and OsPIN1a via OsARF11/16. Both NO - and NH + triggered tiller outgrowth and induced largely overlapping transcriptional responses, with a temporal delay for NO -. Adequate nitrogen supplies induced cytokinin signaling while inhibiting auxin signaling and transport in tiller buds, thereby triggering bud outgrowth. Together, we identify a key regulatory role of auxin-cytokinin antagonistic module for integrating nitrogen signals to determine tiller bud fate.

plant biology↗

bioRxiv2025

PIF4-mediated regulation of H2O2 homeostasis controls Arabidopsis seedling thermomorphogenesis

Thermomorphogenesis under high ambient temperature involves extensive developmental changes, including hypocotyl elongation at the seedling stage, in Arabidopsis. Reactive Oxygen Species (ROS), particularly hydrogen peroxide (H2O2), are important signaling molecules, playing crucial roles in plant development and stress responses. While ROS-homeostasis is shown to be crucial for maintaining cellular functions and mediating various developmental responses, the involvement of ROS-homeostasis in the regulation of thermomorphogenic responses and the underlying genetic basis remains poorly understood. In this study, comprehensive transcriptomic analyses revealed strong induction of ROS homeostasis and signaling genes in Arabidopsis seedlings under high ambient temperature. Pharmacological and genetic experiments showed that maintaining H2O2 homeostasis is crucial for seedling thermomorphogenesis. We identified PHYTOCHROME INTERACTING FACTOR 4 (PIF4) as a key regulator of H2O2 homeostasis via direct transcriptional activation of CAT2 and CAT3 genes, which are involved in the regulation of H2O2 levels, to modulate hypocotyl elongation under high temperature. Genetic and biochemical experiments confirmed that CATs act downstream to PIF4 in the same signaling pathway to regulate high-temperature-responsive hypocotyl elongation. Interestingly, elevated H2O2 levels reduced PIF4 protein abundance under high temperature. Together, our findings establish a PIF4-CAT-H2O2 regulatory module, functioning alongside the canonical PIF4-Auxin module, that integrates to auxin signaling to fine-tune hypocotyl elongation under high temperature by maintaining H2O2 homeostasis. HighlightsO_LIHigh ambient temperature significantly affects ROS homeostasis and signaling genes in Arabidopsis seedlings. C_LIO_LIH2O2 homeostasis is crucial for high-temperature-mediated hypocotyl elongation, a signature feature of Arabidopsis thermomorphogenesis. C_LIO_LIPHYTOCHROME INTERACTING FACTOR 4 (PIF4) regulates the expression of CATALASE genes in a temperature-dependent manner to maintain H2O2 levels for seedling thermomorphogenesis. C_LIO_LIElevated H2O2 level reduces PIF4 protein abundance, thus forming a PIF4-CAT-H2O2 regulatory module that integrates with auxin to fine-tune hypocotyl elongation under high temperature. C_LI

plant biology↗

bioRxiv2025

Integrative comparative transcriptomics using cultivated and wild rice reveals key regulators of developmental and photosynthetic progression along the rice leaf developmental gradient

A comprehensive understanding of gene regulatory networks and the key regulators underlying developmental and physiological progression along the leaf developmental gradient is crucial for optimizing photosynthetic competence. Comparisons of developmental and photosynthetic features across successive leaf developmental stages revealed pronounced differences between wild rice (Oryza australiensis) and three cultivated rice accessions. Global gene expression profiling identified three major transcriptional phases across leaf stages: a predominance of developmental genes at SAM+Pi (initiating primordia) and P3; genes for photosynthetic transition at P3 and P4; and enriched core photosynthetic genes at P4 and P5. O. australiensis showed a more prominent expression of developmental and photosynthetic genes than cultivated accessions across leaf stages. Multivariate analysis further supported a distinct transcriptional landscape in O. australiensis compared with cultivated accessions. Integration of gene expression with species-specific variations in regulatory sequences, derived from synteny-anchored orthology analysis, generated stage-resolved gene regulatory networks and identified key transcription factors (TFs) mediating the developmental and physiological progression. A cross-species comparison of TF-target regulatory networks revealed extensive stage- and accession-dependent rewiring of the regulatory networks of key TFs, with strong regulatory divergence in O. australiensis. Gene silencing of two candidate TFs, OsDOF8 and OsARID2, altered the rice photosynthetic competence with accession-specific effects. Taken together, the study highlights promoter-driven regulatory divergence as a potential mechanism underlying developmental and photosynthetic differences among the rice accessions. The resource is available through an interactive public database, Rice DEV-LEAF (https://nipgr.ac.in/DEV-LEAF/), enabling exploration of gene expression dynamics and regulatory networks across the rice leaf developmental gradient.

plant biology↗

bioRxiv2025

SieveAI: Development of an Automated extensible and customisable drug discovery pipeline and its validation

Systematic Interaction Evaluation and Virtual Enhancement Analysis Interface (SieveAI) is an automated drug discovery pipeline developed to enhance the efficiency of virtual screening and computer-aided drug discovery processes. The molecular docking workflow encompasses acquiring, modeling, and pre-processing of molecular structure files, conducting docking with various algorithms, and subsequent analysis and interpretation of the outcomes by visualising or tabulating the results. While several open-source software tools are available to assist these operations at different steps of molecular docking, they often necessitate manual user intervention at every stage. To streamline and automate this extensive manual process and develop a comprehensive solution, we have developed an innovative, fully extensible, molecular docking pipeline SieveAI ((C)L-129927/2023). The same has been demonstrated in this manuscript. SieveAI works with a range of open-source libraries, packages, and programs to facilitate automated drug discovery using established programs and software. The package is accessible at https://miRNA.in/SieveAI.

bioinformatics↗

bioRxiv2024

Unveiling theranostic potential: Insights into cell-free microRNA-protein interactions

MicroRNAs (miRNAs) belong to a short endogenous class of non-coding RNAs which have been well studied for their crucial role in regulating cellular homeostasis. Their role in modulation of diverse biological pathways by intracellular or extracellular communication and interaction with DNA, RNA or protein, projects them or their targets as promising biomarkers and therapeutic agents. However, studying specific interactions in the extracellular or cell-free environment for drug discovery or biomarker establishment is resource-intensive. In this study, we derive a computational approach based on available experimental data to decipher patterns in miRNA-protein interactions in the cell-free milieu. We characterized the miRNA-protein interactome (miRPin, https://www.mirna.in/miRPin) and identified consensus sequences governing these interactions. The study establishes the role of multiple miRNAs and protein interactions present in cell-free environments leading to pathological conditions, viz., role of proteins like METTL3 and AGO2 etc. and miRNAs like hsa-miR-484 and hsa-miR-30 families, hsa-mir-126-5p etc. in association with multiple miRNAs in different cancer types, cardiovascular diseases, and neurological disorders. The findings outlined in the study may facilitate new avenues of therapeutic discovery leading to the understanding of cellular mechanisms underlying therapy relapse and drug resistance. By addressing these interactions in an extracellular environment may further gain insight into regulating disease initiation and progression, overcoming challenges related to drug efficacy and drug delivery in the presence of bilayer membranes with drug efflux pumps.

bioinformatics↗

bioRxiv2024

The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation

LARP4 interacts with poly(A)-binding protein (PABP) to protect mRNAs from deadenylation and decay, and recent data indicate it can direct the translation of functionally related mRNA subsets. LARP4 was known to bind RACK1, a ribosome-associated protein, although the specific regions involved, and relevance had been undetermined. Here, yeast two-hybrid domain mapping followed by other methods identified positions 615-625 in conserved region-2 (CR2) of LARP4 (and LARP4B) as directly binding RACK1 region 200-317. Consistent with these results, AlphaFold2-multimer predicted high confidence interaction of CR2 with RACK1 propellers 5-6. CR2 mutations strongly decreased LARP4 association with cellular RACK1 and ribosomes by multiple assays, whereas less effect was observed for PABP association, consistent with independent interactions. CR2 mutations decreased LARP4 ability to optimally stabilize a {beta}-globin mRNA reporter containing an AU-rich element (ARE) more significantly than a {beta}-globin and other reporters lacking this element. While polysome profiles indicate the {beta}-glo-ARE mRNA is inefficiently translated, consistent with published data, we show that LARP4 increases its translation whereas the LARP4-CR2 mutant is impaired. Analysis of nanoLuc-ARE mRNA for production of luciferase activity confirmed LARP4 promotes translation efficiency while CR2 mutations are disabling. Thus, LARP4 CR2-mediated interaction with RACK1 can promote translational efficiency of some mRNAs.

molecular biology↗

bioRxiv2024

Specific redox and iron homeostasis responses in the root tip of Arabidopsis upon zinc excess

O_LIZinc (Zn) excess negatively impacts primary root growth in Arabidopsis. Yet, the effects of Zn excess on specific growth processes in the root tip remain largely unexplored. C_LIO_LITranscriptomics, ionomics and metabolomics were used to examine the specific impact of Zn excess on the root tip (RT) compared to the remaining root (RR). C_LIO_LIZn excess exposure resulted in shortened root apical meristem and elongation zone, with differentiation initiating closer to the tip of the root. Zn accumulated at a lower concentration in the RT than in RR. This pattern was associated with lower expression of Zn homeostasis and Fe deficiency response genes. C_LIO_LIA distinct distribution of Zn and Fe in RT and RR was highlighted by Laser Ablation ICP-MS analysis. C_LIO_LISpecialized Trp-derived metabolism genes, typically associated with redox and biotic stress responses, were specifically up-regulated in the RT upon Zn excess, among those Phytoalexin Deficient 3 (PAD3) encoding the last enzyme of camalexin synthesis. In roots of wild-type seedlings, camalexin concentration increased by 6-fold upon Zn excess and a pad3 mutant displayed increased Zn sensitivity and an altered ionome. C_LIO_LIOur results indicate that distinct redox and iron homeostasis mechanisms are key elements of the response to Zn excess in the RT. C_LI

plant biology↗

bioRxiv2024

A multi-omics analysis of Arabidopsis thaliana root tips under Cd exposure: A role of HY5 in limiting accumulation

O_LICadmium (Cd) is a major environmental pollutant with high toxicity potential. Even though a reduction of growth, including the primary root, is a clear consequence of Cd exposure, a profound understanding of the impact of Cd on the root apical meristem (RAM) and the elongation/differentiation zone (EDZ) is still lacking. C_LIO_LIIn this study, Arabidopsis thaliana roots were subjected to Cd and divided into root tips (RT) and remaining roots (RR) to separately assess the effect of Cd using transcriptomics, ionomics and metabolomics. C_LIO_LIElemental profiling revealed lower Cd accumulation in RT and differences in mineral contents between RT and RR. Transcriptomic analysis demonstrated distinct gene expression patterns in RT and RR, with Cd having less impact in RT. Functional enrichment analysis revealed genes associated with iron and sulfur homeostasis as well as the response to light in both RR and RT. RT-specific responses to Cd included several genes regulated by the transcription factor ELONGATED HYPOCOTYL 5 (HY5) and notably, the hy5 mutant showed increased Cd sensitivity and accumulation compared to the wild type. C_LIO_LIThis study provides comprehensive insights into the inhibitory effects of Cd on primary root growth, elucidating molecular mechanisms involved, particularly highlighting the role of HY5 in Cd accumulation. C_LI

plant biology↗

bioRxiv2024

Single nucleus transcriptomics supports a role for CCNA2-induced human adult cardiomyocyte cytokinesis

Cyclin A2 (CCNA2), a master cell cycle regulator silenced in postnatal cardiomyocytes, promotes cardiac repair in animal models. However, its effect on cytokinesis in adult human cardiomyocytes remains unknown. We engineered a replication-deficient adenoviral vector encoding human CCNA2 under the cardiac Troponin T promoter and delivered it to freshly isolated cardiomyocytes from adult human hearts. Time-lapse live imaging revealed induction of complete cytokinesis with preservation of sarcomeres and calcium mobilization in redifferentiated daughter cardiomyocytes. To uncover underlying transcriptional mechanisms, single-nucleus transcriptomics of CCNA2-transgenic versus non-transgenic mouse hearts identified a cardiomyocyte subpopulation enriched for cytokinesis, proliferative, and reprogramming genes. Ultra-deep bulk RNA sequencing of adult and fetal human hearts further highlighted reprogramming pathways relevant to CCNA2-induced effects. Together, these findings demonstrate that CCNA2 can reinitiate cytokinesis in adult human cardiomyocytes and illuminate conserved molecular programs, supporting its promise as a regenerative gene therapy for the heart. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/583057v7_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@b9cfa9org.highwire.dtl.DTLVardef@f0720eorg.highwire.dtl.DTLVardef@1d020b2org.highwire.dtl.DTLVardef@112c28b_HPS_FORMAT_FIGEXP M_FIG C_FIG CCNA2 Induces Cytokinesis and Drives Proliferation and Reprogramming of Adult Cardiomyocytes: An Integrative Transcriptomic Analysis across Human and Mouse Models.

cell biology↗

bioRxiv2024

A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB

RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of [≥]5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>Gand patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.

molecular biology↗

bioRxiv2023

miRVim: Three-dimensional miRNA Structure Data Server

MicroRNAs (miRNAs), a distinct category of non-coding RNAs, exert multifaceted regulatory functions in a variety of organisms, including humans, animals, and plants. The inventory of identified miRNAs stands at approximately 60,000 among all species and 1,926 in Homo sapiens manifests miRNA expression. Their theranostic role has been explored by researchers over the last few decades, positioning them as prominent therapeutic targets as our understanding of RNA targeting advances. However, the limited availability of experimentally determined miRNA structures has constrained drug discovery efforts relying on virtual screening or computational methods, including machine learning. To address this limitation, miRVim has been developed, providing a repository of human miRNA structures derived from both two-dimensional (MXFold2, CentroidFold, and RNAFold) and three-dimensional (RNAComposer and 3dRNA) structure prediction algorithms, in addition to experimentally available structures from the RCSB PDB repository. This data server aims to facilitate computational data analysis for drug discovery, opening new avenues for advancing technologies such as machine learning-based predictions in the field. The publicly accessible structures provided by miRVim, available at https://mirna.in/miRVim, offer a valuable resource for the research community, advancing the field of miRNA-related computational analysis and drug discovery.

bioinformatics↗

bioRxiv2023

Interplay between resource dynamics, network structure and spatial propagation of transient explosive synchronization in an adaptively coupled mouse brain network model

Generalized epileptic attacks, which exhibit widespread disruption of brain activity, are characterized by recurrent, spontaneous and synchronized bursts of neural activity that self-initiate and self-terminate through critical transitions. Here we utilize the general framework of explosive synchronization (ES) from complex systems science to study the role of network structure and resource dynamics in the generation and propagation of seizures. We show that a combination of resource constraint and adaptive coupling in a Kuramoto network oscillator model can reliably generate seizure-like synchronization activity across different network topologies, including a biologically derived mesoscale mouse brain network. The model, coupled with a novel algorithm for tracking seizure propagation, provides mechanistic insight into the dynamics of transition to the synchronized state and its dependence on resources; and identifies key brain areas that may be involved in the initiation and spatial propagation of the seizure. The model, though minimal, efficiently recapitulates several experimental and theoretical predictions from more complex models, and makes novel experimentally testable predictions. Significance statement / Author SummaryUnderstanding seizure dynamics at the whole-brain level is crucial for controlling abnormal hypersynchronous activity. Currently, complete brain coverage recordings are lacking in both patients and animal models. We employ network science tools to investigate epileptic seizure-like synchronization in a mouse whole brain network, leveraging network structure and supported dynamics as the basis for seizure evolution. Our results align with experimental findings, suggesting that seizure activity initiates in the cortico-thalamic circuit. Importantly, our novel analysis identifies key nodes, primarily in the cortex, driving this hypersynchronous activity. Our findings highlight network structures role in shaping seizure dynamics and the techniques developed here could enhance our control of generalized seizures when combined with patient-specific data.

neuroscience↗

bioRxiv2023

Molecular insights into atypical modes of beta-arrestin interaction with seven transmembrane receptors

{beta}-arrestins are multifunctional proteins that are critically involved in regulating spatio-temporal aspects of GPCR signaling. The interaction of {beta}-arrestins with GPCRs is typically conceptualized in terms of receptor activation and phosphorylation primarily in the carboxyl-terminus. Interestingly however, there are several GPCRs that harbor majority of phosphorylation sites in their 3rd intracellular loop (ICL3) instead of carboxyl-terminus but still robustly engage {beta}-arrestins. Moreover, there are several 7TMRs that are now characterized as intrinsically-biased, {beta}-arrestin-coupled receptors (ACRs) due to lack of functional G-protein-coupling but robust {beta}-arrestin binding leading to functional outcomes. The molecular basis of {beta}-arrestin interaction and activation upon binding to these types of 7TMRs is currently elusive, and it represents a major knowledge gap in our current understanding of this signaling system. Here, we present seven cryo-EM structures of {beta}-arrestins in basal state, activated by the muscarinic M2 receptor (M2R) through its ICL3, and a {beta}-arrestin-coupled receptor known as decoy D6 receptor (D6R). These structural snapshots combined with biochemical, cellular, and biophysical experiments including HDX-MS and MD simulation provide novel insights into the ability of {beta}-arrestins to preferentially select specific phosphorylation patterns in the receptors, and also illuminate the structural diversity in 7TMR-{beta}-arrestin interaction. Surprisingly, we also observe that the carboxyl-terminus of {beta}-arrestin2 but not {beta}-arrestin1 undergoes structural transition from a {beta}-strand to -helix upon activation by D6R, which may preclude the core-interaction with the activated receptor. Taken together, our study elucidates previously unappreciated aspects of 7TMR-{beta}-arrestin interaction, and provides important mechanistic clues about how the two isoforms of {beta}-arrestins can recognize and regulate a large repertoire of GPCRs.

biochemistry↗

bioRxiv2023

Peripheral vascular strand development in nodules is controlled by a bHLH/HLH heterodimer

Only the Leguminosae family can develop root nodules with peripheral vasculature, an adaptation that grants them an advantage in optimizing nitrogen fixation efficiency. Medicago truncatula develops indeterminate nodules that possess peripheral vascular-strands encircling the central infection zone. How vascular-strands shifted from the nodule central part to the periphery remains unresolved. Here we show, MtbHLH1 (renamed as Nodule Vascular bundle Development 1) is required for the proper organization of vascular strands. In nvd1 nodules, vascular strands pass through the infection zone. NVD2, an HLH transcription factor that lacks a DNA-binding domain, is activated by NVD1. Mutant nvd2 nodules display a similar partially central vasculature. NVD2 is expressed along the nodule vascular bundle and NVD2:GFP fusion protein localizes to the nodule vascular endodermis. The formation of the peripheral vasculature is dependent on the proper stoichiometry of NVD1 and NVD2 heterodimers, as NVD2 controls NVD1-mediated transcriptional activation by sequestering NVD1. Transcription of NVD1 is activated by auxin and Auxin Responsive transcription Factor (MtARF5). Transcriptome sequencing of nvd1 and nvd2 nodules and visualization of in situ auxin and cytokinin signal outputs indicated aberrant auxin/cytokinin balance in these nodules. Our findings showed that the NVD1-NVD2 heterodimer plays a key role in the formation of an orderly peripheral vascular bundle around Medicago nodules.

plant biology↗

bioRxiv2023

Exploiting the therapeutic vulnerability of IDH-mutant gliomas with zotiraciclib

Isocitrate dehydrogenase (IDH)-mutant gliomas have distinctive metabolic and biological traits that may render them susceptible to targeted treatments. Here, by conducting a high-throughput drug screen, we pinpointed a specific susceptibility of IDH-mutant gliomas to zotiraciclib (ZTR). ZTR exhibited selective growth inhibition across multiple IDH-mutant glioma in vitro and in vivo models. Mechanistically, ZTR at low doses suppressed CDK9 and RNA Pol II phosphorylation in IDH-mutant cells, disrupting mitochondrial function and NAD+ production, causing oxidative stress. Integrated biochemical profiling of ZTR kinase targets and transcriptomics unveiled that ZTR-induced bioenergetic failure was linked to the suppression of PIM kinase activity. We posit that the combination of mitochondrial dysfunction and an inability to adapt to oxidative stress resulted in significant cell death upon ZTR treatment, ultimately increasing the therapeutic vulnerability of IDH-mutant gliomas. These findings prompted a clinical trial evaluating ZTR in IDH-mutant gliomas towards precision medicine (NCT05588141). HighlightsO_LIZotiraciclib (ZTR), a CDK9 inhibitor, hinders IDH-mutant glioma growth in vitro and in vivo. C_LIO_LIZTR halts cell cycle, disrupts respiration, and induces oxidative stress in IDH-mutant cells. C_LIO_LIZTR unexpectedly inhibits PIM kinases, impacting mitochondria and causing bioenergetic failure. C_LIO_LIThese findings led to the clinical trial NCT 05588141, evaluating ZTR for IDH-mutant gliomas. C_LI

cancer biology↗