Biology subjects

Pasmanik-Chor, M.

Publications and source records attributed to Pasmanik-Chor, M..

10 recordsLinked to original sources

bioRxiv2026

Metabolostasis failure thresholds are linked with network topology, metabolite solubility, and translational control

Cells maintain metabolite homeostasis (metabolostasis) by buffering fluctuations in metabolite levels, yet the limits of this buffering and the mechanisms underlying metabolic toxicity remain poorly understood. To study this, we systematically overfed metabolites in Saccharomyces cerevisiae and quantified associations with growth inhibition, intracellular aggregation, and multiomic perturbations. We identify metabolite-specific failure thresholds at which amyloid-like aggregates are observed, with graded growth inhibition detectable at sub-threshold concentrations, suggesting toxicity mechanisms beyond transporter saturation. Metabolites with higher network influence and broader pathway participation are associated with higher failure thresholds and smaller pathway disturbances. These patterns are associated with chemical properties and solubility: more soluble metabolites, while broadly tolerated, are associated with localised aggregates at their failure thresholds, whereas less soluble metabolites are associated with larger systemic pathway disruptions. Multiomic integration identifies a two-tiered translational regulatory architecture characterising cellular resilience to metabolic overfeeding. General resilience is associated with transcriptional commitment to resource conservation via attenuation of anabolic pathways. Metabolite-specific defense is characterised by high-magnitude translational regulatory events; for example, engagement of aromatic catabolism under phenylalanine overfeeding and energetic control pathways under glycine overfeeding. Together, our results operationally define metabolostasis as a cellular system associated with constraint of metabolite concentrations, coordination of network and pathway-level regulation, and buffering against amyloid-like aggregation, highlighting how network topology, pathway architecture, and chemical properties are associated with metabolic resilience and toxicity thresholds.

cell biology↗

bioRxiv2024

Comparative transcriptomic profile reveals candidate genes manipulated by type III effectors of Pantoea agglomerans pv. betae leading to gall formation in beet

Pantoea agglomerans pv. betae (Pab) induces tumor-like galls in beet and gypsophila, a process mediated by the secretion of effector proteins via Pabs type III secretion system (T3SS). The molecular mechanisms underlying Pab-induced gall formation remain largely unexplored. This study delves into the cellular architecture and transcriptional profile of Pab-mediated galls, comparing host responses to wild-type Pab and a T3SS-inactive mutant, hrcC-. Morphological analysis using scanning electron microscopy and cross-sectional visualization of infected beet leaf tissues revealed that Pab-induced gall-like structures are linked to cell hyperplasia and tissue ruptures, contingent on T3SS activity. Comparative transcriptome analysis of wild-type Pab and hrcC- Pab-infected beet leaves at 12 and 48 hours unveiled significant transcriptional reprogramming, with nearly 2,000 differentially expressed genes at 48 hours post inoculation. Enrichment analyses identified the upregulation of pathways related to signal transduction, defense, carbohydrate metabolism, and cell wall modulation in wild-type Pab-infected leaves compared to controls. Particularly notable was the significant upregulation of numerous genes associated with cell wall loosening by wild-type Pab, suggesting an initial rearrangement of cell wall architecture facilitates gall formation. Furthermore, transcriptome analysis demonstrated that wild-type Pab suppresses the expression of the betalain biosynthetic gene DOPA 4,5-DIOXYGENASE, leading to reduced betalain accumulation in infected tissues compared to the mutant strain. These findings offer fresh insights into the transcriptional and physiological manipulation of host tissue during the early stages of Pab-induced gall formation.

plant biology↗

bioRxiv2024

Oligosaccharyltransferase is involved in targeting to ER-associated degradation

Most membrane and secretory proteins undergo N-glycosylation, catalyzed by oligosaccharyltransferase (OST), a membrane-bound complex in the endoplasmic reticulum (ER). Proteins failing quality control are degraded via ER-associated degradation (ERAD), involving retrotranslocation to cytosolic proteasomes. Using SILAC proteomics, we identified OST subunits as key interactors with a misfolded ER protein bait, suggesting unexpected involvement in ERAD. Previous reports implied additional roles for OST subunits beyond N-glycosylation, such as quality control by ribophorin I. We tested OST engagement in glycoprotein and non-glycosylated protein ERAD; overexpression or partial knockdown of OST subunits interfered with ERAD in conditions that did not affect glycosylation. Effects were studied on misfolded membrane proteins, BACE476 and asialoglycoprotein receptor H2a, and the luminal 1-antitrypsin NHK variant. OST appears to participate in late ERAD stages, interacting with the E3 ligase HRD1 and facilitating retrotranslocation. Molecular dynamics simulations suggest membrane thinning by OST transmembrane domains, possibly assisting retrotranslocation via membrane distortion.

cell biology↗

bioRxiv2023

Calcium regulation of the Arabidopsis Na+/K+ transporter HKT1;1 improves seed germination under salt stress

Calcium is known to improve seed-germination rates under salt stress. We investigated the involvement of calcium ions (Ca2+) in regulating HIGH-AFFINITY K+ TRANSPORTER 1 (HKT1;1), which encodes a Na+/K+ transporter, and its post-translational regulator TYPE 2C PROTEIN PHOSPHATASE 49 (PP2C49), in germinating Arabidopsis thaliana seedlings. Germination rates of hkt1 mutant seeds under salt stress remained unchanged by CaCl2 treatment in wild-type Arabidopsis, whereas pp2c49 mutant seeds displayed improved salt-stress tolerance in the absence of CaCl2 supplementation. Analysis of HKT1;1 and PP2C49 promoter activity revealed that CaCl2 treatment results in radicle-focused expression of HKT1;1 and reduction of the native radicle-exclusive expression of PP2C49. Ion-content analysis indicated that CaCl2 treatment improves K+ retention in germinating wild-type seedlings under salt stress, but not in hkt1 seedlings. Transgenic seedlings designed to exclusively express HKT1;1 in the radicle during germination displayed higher germination rates under salt stress than the wild type in the absence of CaCl2 treatment. Transcriptome analysis of germinating seedlings treated with CaCl2, NaCl, or both revealed 118 upregulated and 94 downregulated genes as responsive to the combined treatment. Bioinformatics analysis of the upstream sequences of CaCl2-NaCl-treatment-responsive upregulated genes revealed the abscisic acid response element CACGTGTC, a potential CaM-binding transcription activator-binding motif, as most prominent. Our findings suggest a key role for Ca2+ in mediating salt-stress responses during germination by regulating genes that function to maintain Na+ and K+ homeostasis, which is vital for seed germination under salt stress.

plant biology↗

bioRxiv2023

Serine peptidases and increased amounts of soluble proteins contribute to heat priming of the plant pathogenic fungus Botrytis cinerea

Botrytis cinerea causes grey mold disease in leading crop plants. The disease develops only at cool temperatures, but the fungus remains viable in warm climates and can survive periods of extreme heat. We discovered a strong heat priming effect in which the exposure of B. cinerea to moderately high temperatures greatly improves its ability to cope with subsequent, potentially lethal temperature conditions. We showed that priming promotes protein solubility during heat stress and discovered a group of priming-induced serine-type peptidases. Several lines of evidence, including transcriptomics, proteomics, pharmacology, and mutagenesis data, link these peptidases to the B. cinerea priming response, highlighting their important roles in regulating priming-mediated heat adaptation. By imposing a series of sub-lethal temperature pulses that subverted the priming effect, we managed to eliminate the fungus and prevent disease development, demonstrating the potential for developing temperature-based plant protection methods by targeting the fungal heat priming response. ImportancePriming is a general and important stress adaptation mechanism. Our work highlights the importance of priming in fungal heat adaptation, reveals novel regulators and aspects of heat adaptation mechanisms, and demonstrates the potential of affecting microorganisms, including pathogens through manipulations of the heat adaptation response.

microbiology↗

bioRxiv2022

Epigenetic aging waves:Artificial intelligence detects clustering of switch points in DNA methylation rate in defined sex-dependent age periods

BackgroundAging is linked to hypermethylation of CpG sites on promoters and enhancers, along with loss of methylation in intergenic zones. That such changes are not necessarily a continuous process is exemplified by the extensive changes in DNA methylation during development with another significant time of change during adolescence. However, the relation between age and DNA methylation during adult life has not been systematically evaluated. In particular, potential changes in methylation trends in the same CpGs over the years that may occur with aging remain largely unexplored. MethodsHere we set out to determine the average trends by age of the CpG sites represented in the Illumina 450 platform, based on data from 2143 subjects of the age range of 20 to 80 years, compiled from 24 different cohorts. Using several mathematical procedures, we initially separated stationary probes from probes whose methylation changes with age. Among the latter, representing [~]20% of the probes, we then focused on the identification of CpG sites with switch points, i.e., a point where a stable trend of change in the age-averaged methylation is replaced by another linear trend. ResultsUsing several mathematical modeling steps, we generated a machine learning model that identified 5175 CpG sites with switch points in age-related changes in the trend of methylation over the years. Switch points reflect acceleration, deceleration or change of direction of the alteration of methylation with age. The 5175 switch points were limited to 2813 genes in three waves, 80% of which were identical in men and women. A medium-size wave was seen in the early forties, succeeded by a dominant wave as of the late fifties, lasting up to 8 years each. Waves appeared[~]4-5 years earlier in men. No switch points were detected on CpGs mapped to the X chromosome. ConclusionIn non-stationary CpG sites, concomitant switch points in age related changes in methylations can be seen in a defined group of sites and genes, which cluster in 3 age- and sex-specific waves.

genomics↗

bioRxiv2022

Tomato brassinosteroid-signaling kinase Bsk830 is a component of flagellin signaling that regulates pre-invasion immunity

Detection of bacterial flagellin by the tomato receptors Flagellin sensing 2 (Fls2) and Fls3 triggers activation of pattern-triggered immunity (PTI). Tomato signaling components associated or downstream of flagellin receptors are largely unknown. We investigated the involvement of tomato brassinosteroid-signaling kinase 830 (Bsk830) in PTI triggered by flagellin perception. Bsk830 localized to the plasma membrane and interacted with Fls2 and Fls3. Consistent with a role in flagellin- induced signaling, CRISPR/Cas9-generated tomato bsk830 mutants were impaired in ROS accumulation induced by the flagellin-derived flg22 and flgII-28 peptides. In addition, bsk830 mutants developed larger populations of Pseudomonas syringae pv. tomato (Pst) strain DC3000 than wild-type plants, whereas no differences were observed in plants infected with the flagellin deficient Pst DC3000{Delta}fliC. bsk830 mutants failed to close stomata when infected with Pst DC3000 and Pseudomonas fluorescens, and were more susceptible to Pst DC3000 than wild-type plants when inoculated by dipping, but not by vacuum-infiltration, indicating involvement of Bsk830 in pre-invasion immunity. Analysis of gene expression profiles in bsk830 mutants detected a reduced number of differentially expressed genes and altered expression of jasmonic acid (JA)-related genes. In support of deregulation of JA response in bsk830 mutants, these plants were similarly susceptible to Pst DC3000 and to the Pst DC3118 strain, which is deficient in coronatine production, and more resistant to the necrotrophic fungus Botrytis cinerea following PTI activation. These results indicate that tomato Bsk830 is required for a subset of flagellin-triggered PTI responses and support a model in which Bsk830 negatively regulates JA signaling during PTI activation.

plant biology↗

bioRxiv2022

Kynurenic acid, a key L-tryptophan-derived metabolite, protects the heart from an ischemic damage

BackgroundRenal injury induces major changes in plasma and cardiac metabolites. We sought to identify a key metabolite that may affect cardiac mitochondria following an acute kidney injury (AKI) that may be harnessed to protect the heart following an acute ischemic event. Methods and ResultsMetabolomics profiling of cardiac lysates and plasma samples derived from rats that underwent AKI 1 or 7 days earlier by 5/6 nephrectomy versus sham-operated controls was performed. We detected only 26 differential metabolites in both heart and plasma samples at the two selected time points, relative to sham. Out of which, kynurenic acid (kynurenate, KYNA) seemed most relevant. Interestingly, KYNA given at 10 mM concentration significantly rescued the viability of H9C2 cardiac myoblast cells grown under anoxic conditions and largely improved their mitochondrial structure and function as determined by flow cytometry and cell staining with MitoTracker dyes. Moreover, KYNA diluted in the drinking water of animals induced with an acute myocardial infarction, highly enhanced their cardiac recovery according to echocardiography and histopathology. Conclusion and translational aspectKYNA may represent a key metabolite absorbed by the heart following AKI. This metabolite can enhance cardiac cell viability following an ischemic event in a mechanism that is mediated, at least in part, by the protection of the cardiac mitochondria. A short-term administration of KYNA may be highly beneficial in the treatment of the acute phase of kidney disease in order to attenuate progression to CRS and in ischemic cardiac conditions to reduce ischemic myocardial damage. HighlightsO_LIThe levels of the L-Tryptophan-derived metabolite, Kynurenic acid (KYNA), are significantly elevated in the heart and the plasma of animals induced with an acute kidney disease. C_LIO_LIKYNA rescues the viability of cardiac cells from an ischemic damage both in vitro and in vivo. C_LIO_LIKYNA can protect the structure & function of cardiac mitochondria in H9C2 cardiomyoblast cells upon exposure to anoxia. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=140 HEIGHT=200 SRC="FIGDIR/small/492275v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@f2a49aorg.highwire.dtl.DTLVardef@14a501org.highwire.dtl.DTLVardef@15d016aorg.highwire.dtl.DTLVardef@10800e7_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2021

Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns

BackgroundThe epigenetic age can now be extrapolated from one of several epigenetic clocks, which are based on age-related changes in DNA methylation levels at specific multiple CpG sites. Accelerated aging, calculated from the discrepancy between the chronological age and the epigenetic age, has shown to predict morbidity and mortality rate. We assumed that deconvolution of epigenetic age to its components could shed light on the diversity of epigenetic, and by inference, on inter-individual variability in the causes of biological aging. ResultsUsing the Horvath original epigenetic clock, we identified several CpG sites linked to distinct genes that quantitatively explain much of the interpersonal variability in epigenetic aging, with CpG sites related to secretagogin and malin being the most variable. We show that equal epigenetic age in different subjects can result from variable contribution size of the same CpG sites to the total epigenetic age. In a healthy cohort, the most variable CpG sites are responsible for accelerated and decelerated epigenetic aging, relative to chronological age. ConclusionsOf the 353 CpG sites that form the basis for the Horvath epigenetic age, we have found the CpG sites that are responsible for accelerated and decelerated epigenetic aging in healthy subjects. However, the relative contribution of each site to aging varies between individuals, leading to variable personal aging patterns. Our findings pave the way to form personalized aging cards allowing the identification of specific genes related to CpG sites, as aging markers, and perhaps treatment of these targets in order to hinder undesirable age drifting.

developmental biology↗

bioRxiv2019

Uncoating of COPII from ER exit site membranes precedes cargo accumulation and membrane fission

COPII and COPI are considered to be analogous sets of vesicle coat protein heterocomplexes. Coupled to cargo selection, they mediate the formation of membrane vesicles translocating in opposite directions to differ rent destinations within the secretory pathway. Here, live cell and electron microscopy provided evidence for a different localization and mode of function of the COPII coat during protein export from the endoplasmic reticulum (ER). Pharmaceutical and genetic perturbations of ER-Golgi transport were used to demonstrate that COPII is recruited to membranes defining the boundary of ER-ER Exit Sites (ERES) where it facilitates selective cargo concentration. Uncoating of COPII membranes precedes cargo accumulation and fission of Golgi-bound carriers. Moreover, we report what may be direct transfer of cargo to the Golgi apparatus from Golgi-associated BFA sensitive ERESs. Finally, in ldlF cells the stably expressed functional {varepsilon}-COPI-EYFP labeled both ERESs and anterograde carriers. These findings change our understanding of the role of coat proteins in ER to Golgi transport.

cell biology↗