Biology subjects

Thirumlaikumar, V. P.

Publications and source records attributed to Thirumlaikumar, V. P..

6 recordsLinked to original sources

bioRxiv2026

Hopeaphenol targets histidine kinase signaling across kingdoms to suppress bacterial virulence and potentiate plant immunity

Small molecules can control plant disease either by disarming the pathogen or by priming host immunity, but single compounds that do both are rare and mechanistically unexplained. Here we show that hopeaphenol (HP), a resveratrol tetramer from stilbene producing plants, acts on histidine kinase (HK) signaling on both sides of the Arabidopsis-Pseudomonas interaction. In Pseudomonas syringae pv. tomato DC3000, HP represses the type III secretion regulon and motility genes, restricts surface motility independently of effector delivery, and binds a defined subset of virulence-associated sensor kinases while reducing their autophosphorylation; comparable engagement occurs in Pectobacterium atrosepticum. Binding and inhibition depend on the tetrameric scaffold rather than the resveratrol monomer. In the host, HP binds the CHASE domains of the cytokinin receptors AHK2, AHK3 and AHK4 and elicits an immune-associated, rather than canonical cytokinin, transcriptional output. HP-dependent potentiation of PTI and ETI responses and early restriction of bacterial growth require AHK3 and AHK4. HP thus coordinates opposing outputs from divergent HK systems across kingdoms.

plant biology↗

bioRxiv2026

Translocon Remodeling Modulates Ribosomal Frameshifting and the Maturation of the Sindbis Virus Structural Polyprotein

Like other enveloped RNA viruses, alphaviruses synthesize and assemble their envelope glycoproteins at the endoplasmic reticulum (ER) membrane. There, protein-conducting channels called translocons provide nascent proteins access to the membrane and allow them to fold into their correct shapes. We previously showed that a hydrophobic segment in the Sindbis virus structural polyprotein forms cotranslational interactions with the translocon that enhance -1 programmed ribosomal frameshifting (-1PRF), a recoding event that regulates polyprotein biogenesis. Recent discoveries concerning translocon remodeling suggest this segment, which corresponds to the second transmembrane domain of the E2 protein, could serve as a signal that recruits the multipass translocon (MPT). Here, we show that knocking out certain components of the MPT increases -1PRF efficiency. These differences in recoding coincide with changes in the membrane topology of the nascent polyprotein and in its downstream proteolytic processing in a manner that ultimately reduces viral fitness. Together, our results indicate that -1PRF and spike protein maturation in alphaviruses is tuned by the dynamic remodeling of the ER translocon. Such coupling could allow polyprotein biogenesis to adapt to different stages of viral replication and to distinct host or vector environments.

molecular biology↗

bioRxiv2026

Thiol depletion and disruption of proteostasis contribute to the phytotoxicity of juglone

O_LIJuglone is the phytotoxic 1,4-naphthoquinone responsible for the allelopathic effects of black walnut (Juglans nigra), yet how plants perceive and respond to juglone remain poorly understood. C_LIO_LIWe conducted transcriptome profiling of rosettes and roots of Arabidopsis thaliana exposed to juglone from 30 min to 5 d, along with targeted metabolic profiling, biochemical assays, and untargeted proteomics to gain a systems-level understanding of how plants respond to juglone and to test hypotheses underlying its phytotoxicity. C_LIO_LIJuglone exposure induced expression of genes involved in glutathione, cysteine, and sulfur metabolism pathways, and in protein homeostasis. We found that juglone depletes the pool of reduced glutathione (GSH) in roots, in part, through conjugation. We demonstrate that via upregulation of transcription factors (NAC53 and NAC78), the response to juglone activates components of the proteasome stress regulon and triggers extensive proteome remodeling with engagement of the autophagy pathway when proteasome capacity is limited. C_LIO_LIOur findings (i) indicate that thiol depletion and disruption of proteostasis through juglones dual redox cycling and alkylation activities are central to its phytotoxicity, (ii) cast doubt on previous reports that juglone targets a specific enzyme in plants or other organisms, and (iii) provide insight into how the chemical properties of allelopathic quinones shape their ecological roles. C_LI

plant biology↗

bioRxiv2024

Small molecule oxybutynin rescues proliferative capacity of complex III-defective MPCs

Mitochondrial disease encompasses a group of genetically inherited disorders hallmarked by an inability of the respiratory chain to produce sufficient ATP. These disorders present with multisystemic pathologies that predominantly impact highly energetic tissues such as skeletal muscle. There is no cure or effective treatment for mitochondrial disease. We have discovered a small molecule known as oxybutynin that can bypass Complex III mitochondrial dysfunction in primary murine and human skeletal muscle progenitor cells (MPCs). Oxybutynin administration improves MPC proliferative capacity, enhances cellular glycolytic function, and improves myotube formation. Mechanistically, results from our isothermal shift assay indicates that oxybutynin interacts with a suite of proteins involved in mRNA processing which then trigger the upregulation biological pathways to circumvent CIII mitochondrial dysfunction. Taken together, we provide evidence for the small molecule oxybutynin as a potential therapeutic candidate for the future treatment of CIII mitochondrial dysfunction.

cell biology↗

bioRxiv2024

Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing

In agriculture, mineral nutrients uptake and deposition profoundly influence plant development, stress resilience, and productivity. Despite its classification as a non-essential element, silicon (Si) is crucial in plant physiology, particularly in defense response and stress mitigation. While genetic and molecular mechanisms of Si uptake and transport are well-studied in monocots, particularly rice, its role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. Traditional bulk transcriptomics methods lack the resolution to uncover cellular heterogeneity. Here, we present a study by utilizing single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. Our analysis revealed distinct cellular populations, including a novel Si-induced cell cluster within vascular cells, suggesting a specific mechanism of Si distribution. Si treatment induced the expression of defense-related genes, particularly enriched in vascular cells, highlighting their specialized role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in RNA silencing, phytoalexin biosynthesis, and immune receptor signaling, suggesting a mechanism of transcriptional priming of genes involved in defense responses. We further investigated putative Si transporters, revealing differential expression patterns in response to Si treatment, suggesting presence of active and gradient-based transport mechanisms. Our findings shed light on the vital biotic stress regulatory networks governed by Si treatment in soybean leaves, paving potential strategies for enhancing stress tolerance and agronomic performance in crops.

plant biology↗

bioRxiv2024

Mapping protein-metabolite interactions in E. coli by integrating chromatographic techniques and co-fractionation mass spectrometry.

In our pursuit of understanding the protein-metabolite interactome, we introduced PROMIS, a co-fractionation mass spectrometry (CF-MS) technique focusing on biosynthetic and regulatory processes. However, the challenge lies in distinguishing true interactors from coincidental co-elution when a metabolite co-fractionates with numerous proteins. To address this, we integrated two chromatographic techniques-- size exclusion and ion exchange--to enhance the mapping of protein-metabolite interactions (PMIs) in Escherichia coli. This integration aims to refine the PMI network by considering size and charge characteristics, resulting in 994 interactions involving 51 metabolites and 465 proteins. The PMI network is enriched for known and predicted interactions validating our approachs efficacy. Furthermore, the analysis of protein targets for different metabolites revealed novel functional insights, such as the connection between proteinogenic dipeptides and fatty acid biosynthesis. Notably, we uncovered an inhibitory interaction between the riboflavin degradation product lumichrome and orotate phosphoribosyltransferase (PyrE), a key enzyme in de novo pyrimidine synthesis. Lumichrome supplementation mimicked the biofilm formation inhibition observed in a{Delta} pyrE mutant strain, suggesting lumichrome role in integrating pyrimidine and riboflavin metabolism with quorum sensing and biofilm formation. In summary, our integrated chromatographic approach significantly advances PMI mapping, offering novel insights into functional associations and potential regulatory mechanisms in E. coli.

biochemistry↗