Copper Stress Trigger Organelles Communication and Chromatin Condensation Leading to Cell Death in Solanum lycopersicum

Copper Stress Trigger Organelles Communication and Chromatin Condensation Leading to Cell Death in Solanum lycopersicum | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Copper Stress Trigger Organelles Communication and Chromatin Condensation Leading to Cell Death in Solanum lycopersicum Sakshi Chouhan , Shilpa Chandra , Abdul Salam , Chayan Kanti Nandi doi: https://doi.org/10.1101/2025.07.17.665307 Sakshi Chouhan 1 School of Chemical Science, Indian Institute of Technology Mandi , HP-175005 Find this author on Google Scholar Find this author on PubMed Search for this author on this site Shilpa Chandra 2 Indian Knowledge System and Mental Health Applications Centre, Indian Institute of Technology Mandi , HP-175005 Find this author on Google Scholar Find this author on PubMed Search for this author on this site Abdul Salam 1 School of Chemical Science, Indian Institute of Technology Mandi , HP-175005 Find this author on Google Scholar Find this author on PubMed Search for this author on this site Chayan Kanti Nandi 1 School of Chemical Science, Indian Institute of Technology Mandi , HP-175005 2 Indian Knowledge System and Mental Health Applications Centre, Indian Institute of Technology Mandi , HP-175005 Find this author on Google Scholar Find this author on PubMed Search for this author on this site For correspondence: chayan{at}iitmandi.ac.in Abstract Full Text Info/History Metrics Supplementary material Preview PDF Abstract Copper (Cu) is a vital micronutrient for plants but becomes highly toxic when present in excess, disrupting redox balance and damaging cellular structures. While the physiological and mitochondrial responses to Cu toxicity are well-documented, the nuclear-level consequences, particularly chromatin remodeling and gene regulatory changes, remain poorly understood. In this study, we used the root apex of Solanum lycopersicum as a model system to explore how increasing copper concentrations affect organelle integrity, stress signaling, and nuclear architecture. Using confocal and super-resolution imaging with organelle-specific markers and immunostaining, we observed that mitochondria was the earliest affected to Cu stress, exhibiting fragmentation, membrane depolarization, and cytochrome c release led to reactive oxygen species (ROS) accumulation, activation of AMPK, suppression of mTOR signaling, and nuclear translocation of NRF2. Critically, we found that copper exposure induced profound nuclear alterations, including shrinkage, lobulation, peripheral chromatin tethering, and global condensation events tightly correlated with stress signaling. H3K4me3 immunostaining revealed a shift from active euchromatin to condensed, transcriptionally silent states, leading to membrane rupture and cell death in root tip cells. Our findings show that the nucleus actively integrates organelle-derived stress signals, with chromatin remodeling as a key marker of copper toxicity. This highlights potential for chromatin-based diagnostics and stress-resilient crop breeding. Download figure Open in new tab Introduction Copper (Cu) is an essential micronutrient required for numerous physiological and biochemical processes in plants, including mitochondrial respiration, antioxidant defence, iron mobilization, and photosynthetic electron transport 1 – 5 . As a redox-active metal, copper serves as a catalytic cofactor for critical enzymes such as cytochrome c oxidase, Cu/Zn-superoxide dismutase, and laccases 6 – 8 . However, this same redox activity makes excess copper highly toxic, primarily through the generation of reactive oxygen species (ROS), which inflict damage on lipids, proteins, and nucleic acids 9 . Over the past decade, anthropogenic activities including mining, industrial waste discharge, and excessive use of copper-based agrochemicals have led to elevated levels of copper in soil and water, prompting intensive research into its toxicological impacts on plant growth and cellular function 10 . Numerous studies have documented the adverse effects of copper toxicity on seed germination, root and shoot elongation, chlorophyll biosynthesis, and photosynthetic efficiency 11 – 13 . At the cellular level, copper induces oxidative bursts, resulting in ROS accumulation, membrane disruption, protein oxidation, and DNA damage 14 . These stressors trigger a suite of antioxidant responses involving superoxide dismutase (SOD), catalase, and ascorbate peroxidase 15 . Despite extensive research on the physiological, biochemical, and even mitochondrial responses to copper toxicity, very limited attention has been given to the nucleus the master regulator of stress-responsive gene expression and to chromatin-level changes in plants under copper stress 16 . While drought, salt, and other abiotic stresses are known to influence nuclear morphology, chromatin compaction, and histone modifications, similar investigations under heavy metal stress, especially copper, remain scarce 17 . In animal, copper has been implicated in mitochondrial dysfunction, cytochrome c release, and redox imbalance, but nuclear-level disruptions remain underexplored 18 . A few studies on metals like cadmium and aluminum have shown that heavy metals can influence nucleosome positioning, histone methylation, and global transcription patterns, yet comparable mechanisms under copper stress particularly in agriculturally relevant species like Solanum lycopersicum have not been systematically investigated 19 , 20 . Although copper’s uptake, translocation, and detoxification in plants have been well studied, the downstream nuclear consequences, especially alterations in chromatin organization and nuclear architecture, remain poorly understood 21 . This creates a major gap in our understanding of how copper-induced stress is perceived and transduced at the genomic level, where transcriptional reprogramming is ultimately orchestrated. This study aims to fill this critical knowledge gap by focusing on nuclear structure and chromatin remodeling as central mediators rather than passive endpoints of copper-induced stress responses 22 . We utilized the root apex of tomato ( Solanum lycopersicum ) as a model due to its sensitivity to environmental cues and its well-defined zones of cellular activity. By combining high-resolution imaging with organelle-specific fluorescent markers and immunostaining techniques, we evaluated how increasing doses of copper affect nuclear morphology and chromatin distribution 23 . To visualize these subcellular changes with precision, we employed confocal microscopy for volumetric organelle imaging and Super-Resolution Radial Fluctuations (SRRF) to resolve fine chromatin structures and nuclear envelope details beyond the diffraction limit 24 . To establish a mechanistic link between copper exposure and nuclear responses, we simultaneously examined mitochondria (for structural damage, membrane potential, cytochrome c release), ROS accumulation, lysosomal activity (autophagy), and energy/redox signaling markers (AMPK, mTOR, NRF2) 25 – 27 . These multi-organelle indicators allowed us to corroborate that chromatin rearrangement is a direct consequence of systemic copper-induced stress and not merely a secondary or isolated nuclear phenomenon. We observed profound nuclear alterations in root tip cells under copper stress, including nuclear shrinkage, lobulation, chromatin condensation, and peripheral heterochromatinization all indicative of suppressed transcriptional activity. These nuclear changes occurred in parallel with mitochondrial dysfunction, ROS buildup, and activation of lysosome-dependent autophagy pathways. Additionally, activation of AMPK, inhibition of mTOR, and nuclear translocation of NRF2 pointed to disrupted energy homeostasis and redox signaling. Taken together, these findings support the central role of the nucleus as an integrator of environmental stress signals, rather than a passive responder. Our results not only highlight nuclear architecture as an early and sensitive indicator of copper toxicity but also open new avenues for developing chromatin-based biomarkers for environmental monitoring and stress-resilient crop breeding. Results We cultivated Solanum lycopersicum under controlled conditions and exposed them to varying concentrations of copper for 24 hours to induce differential concentration. To assess subcellular effects, we used confocal and SRRF imaging with organelle- and nucleus-specific fluorescent probes and immunostaining. MitoTracker Green (MTG) and TMRE were used to evaluate mitochondrial morphology and membrane potential, while cytochrome c immunostaining detected its release into the cytosol, indicating apoptosis initiation 28 – 30 . Lysosomal activity was tracked with LysoTracker Red (LTR) 31 . Immunostaining for AMPK and mTOR revealed energy stress signaling and non-canonical nuclear mTOR accumulation 32 . NRF2 immunostaining demonstrated ROS-induced nuclear translocation 33 , 34 . Nuclear integrity and chromatin remodeling were assessed via DAPI, Hoechst, and H3K4me3 staining 35 – 37 . PI staining marked late-stage cell death 38 . This integrative approach enabled high-resolution mapping of copper-induced organelle dysfunction, nuclear changes, and cell fate in tomato root apex cells. Additionally, we have checked physiological changes in the root and shoot system (Supplementary Figures 1) 39 . 1. Early Mitochondrial Collapse and Pro-Apoptotic Signaling Triggered by Copper Exposure We analyzed mitochondria because they are the primary sites of copper-induced oxidative stress and energy disruption 40 . Early issues with mitochondria are a big reason for stress signals in the cell, which include making reactive oxygen species (ROS), starting cell death (apoptosis), and changes in the cell’s nucleus 41 – 43 . Exposure to increasing concentrations of copper led to progressive deterioration of mitochondrial integrity in tomato root apex cells, marking the first detectable signal of cellular distress. MitoTracker Green (MTG) staining showed a clear loss of the typical mitochondrial network, with dysfunctional and fading signals as copper levels increased ( Figure 1 Ia-f ) 28 . This was accompanied by a noticeable drop in mitochondrial membrane potential, shown by the decrease in TMRE fluorescence 30 . In control cells, the signals from MTG and TMRE were evenly spread throughout the root meristem, showing that the mitochondria were healthy and functioning properly ( Figure 1 Ia ) . However, as copper levels increased, the TMRE signal decreased much earlier than the MTG signal, indicating that the mitochondria start to malfunction before they lose their structure ( Figure 1 Ib-f ) . At the same time, cytochrome c (CytC) was found in small spots linked to mitochondria in control samples, but it spread out and moved into the cytoplasm, especially with moderate to high copper exposure ( Figure 2 Ia-f ) 29 . This release of CytC into the cytoplasm fluid is a key sign that the outer membrane of the mitochondria is breaking down and that the process of cell death is starting. Line profile analyses further validated the spatial separation of MTG and CytC signals under stress conditions, confirming that CytC dissociates from fragmented mitochondrial compartments ( Figure 1 & 1 & 2 IV-V ) . Quantitative measurements revealed a consistent decrease in MTG and TMRE signal intensity, coupled with a significant rise in CytC fluorescence, establishing a strong correlation between mitochondrial breakdown and early apoptotic signaling ( Figures 1 & 2 II-III ) . These findings demonstrate that mitochondrial dysfunction, manifested as membrane depolarization and cytochrome c release, is the first physiological disturbance triggered by copper toxicity, setting off the downstream cascade of stress responses 27 . This event is the first signal that something is wrong, acting as the primary intracellular alarm leading for copper stress to nuclear and cellular remodeling. Download figure Open in new tab Figure 1. Copper stress leads to mitochondrial membrane depolarization in tomato root apex cells. (I) Confocal images show MTG (green) and TMRE (red) staining across increasing copper concentrations. Control cells display strong TMRE signal co-localized with MTG, indicating healthy, polarized mitochondria. Under copper stress, TMRE signal diminishes progressively, while MTG signal remains, indicating loss of membrane potential. (II–III) Quantification shows a dose-dependent decrease in TMRE intensity with relatively stable MTG levels. (IV–V) Line profiles confirm reduced TMRE signal relative to MTG under stress. (VI–VIII) Bar graphs show reduced mitochondrial area, TMRE-positive cells, and TMRE/MTG ratio, confirming early mitochondrial depolarization under copper stress. Scale bars: 50□µm. Data represent mean ± SEM, n = 10 root tips per condition. Download figure Open in new tab Figure 2. Copper stress triggers mitochondrial damage and cytochrome c release in tomato root apex cells. (I) Confocal images show dose-dependent mitochondrial dysfunction (MTG, green) and increased cytochrome c release (Cyt C, red) from mitochondria into the cytosol. (II–III) Quantification reveals a rise in Cyt C intensity and a decline in MTG signal with increasing copper concentration. (IV–V) Line profiles confirm Cyt C displacement and MTG signal loss, indicating early mitochondrial dysfunction and initiation of apoptotic signaling. Scale bars: 50□µm. Data represent mean ± SEM, n = 10 root tips per condition. 2. Mitochondrial Dysfunction Leads to ROS Accumulation and NRF2-Mediated Nuclear Signaling After mitochondrial dysfunction, exposure to copper caused a significant rise in reactive oxygen species (ROS) levels in the tip cells of tomato roots, showing that mitochondria are a key source of oxidative burst 42 . As shown in Figure 3 , ROS-specific fluorescent dye staining revealed minimal fluorescence in control cells 34 . The signal became stronger as the amount of copper increased, and measurements showed a significant rise in ROS levels with higher copper concentrations. Line profile analysis showed how ROS is spread out, with high intensity peaks in areas experiencing strong mitochondrial stress, suggesting that damaged mitochondria are the main source of ROS production ( Figure 3 III ) . This ROS surge likely contributes to oxidative damage to lipids and proteins, but more critically, it acts as a secondary messenger, activating downstream redox-sensitive pathways 9 . Download figure Open in new tab Figure 3. Copper stress induces ROS accumulation and NRF2 nuclear translocation in tomato root apex cells. (I) H□DCFDA staining shows a dose-dependent increase in ROS levels under copper treatment. (II–III) Quantification and line profile confirm elevated ROS, especially at 250□µM. (IV) Confocal images show NRF2 translocation from cytoplasm to nucleus, confirmed by DAPI co-staining and zoomed views. (V–VII) Box plots and co-localization analysis (M1, M2, PCC) support increased nuclear NRF2 accumulation and chromatin condensation. Scale bars: 50□µm & 2□µm. Data: mean ± SEM, n = 10 root tips. The transcription factor NRF2 mediates one such response, and Figure 3 IV uses immunofluorescence to visualize its activation under oxidative stress 33 . In control cells, NRF2 exhibited a weak, diffuse cytoplasmic signal with minimal nuclear localization ( Figure 3 IVa ) . NRF2 fluorescence became noticeably nuclear-enriched after being treated with copper, especially in the early root apex zones. High-resolution insets and DAPI co-staining confirmed NRF2 translocation into the nucleus ( Figure 3 IVb-f ) 36 . This change shows the typical redox regulation process, where ROS help keep NRF2 from breaking down, letting it build up and move into the nucleus 44 . Quantitative analysis revealed a significant increase in the nuclear-to-cytoplasmic ratio of NRF2 signal across copper concentrations ( Figure 3 V-VI ) . These results indicate that oxidative stress connects damage to mitochondria with the cell’s response in the nucleus, with NRF2 playing an important role in helping the cell adapt by turning on stress-related genes. This translocation likely initiates protective antioxidant gene expression while also priming the nucleus for broader chromatin remodeling in response to sustained cellular damage. 3. Copper-induced oxidative stress reprograms redox-energy signaling by activating AMPK and promoting the non-canonical nuclear accumulation of mTOR To investigate the metabolic response to oxidative stress triggered by copper, we examined the activation of AMP-activated protein kinase (AMPK) and its downstream target mTOR in tomato root apex cells 45 , 46 . As shown in Figure 4 , immunostaining of phosphorylated AMPK (pAMPK) revealed a low basal level in control cells, where fluorescence remained diffuse and weak across the cytoplasm ( Figure 4 Ia ) 32 . Upon exposure to increasing copper concentrations, the pAMPK signal intensified significantly and became enriched in both the cytoplasm and nucleus, indicating activation under energy-deprived conditions ( Figure 4 Ib-f ) . Quantitative analysis confirmed a strong dose-dependent increase in pAMPK intensity, reflecting cellular energy stress and metabolic reprogramming ( Figure 4II-V ) . Download figure Open in new tab Figure 4. Copper stress activates AMPK and disrupts mitochondrial integrity in tomato root apex cells. (I) Confocal images show mitochondrial structure (MTG, green) and AMPK (red) localization under increasing copper concentrations. (II–III) Quantification reveals dose-dependent AMPK activation and a decline in MTG signal. (IV–V) Line profiles confirm increased AMPK intensity and reduced mitochondrial mass under stress, indicating energy sensing activation coupled with mitochondrial dysfunction. Scale bars: 50□µm. Data represent mean ± SEM, n = 10 root tips per condition. In parallel, we observed a marked suppression of mTOR expression under copper treatment ( Figure 5 ) . In control root cells, mTOR signal was predominantly cytoplasmic and enriched in actively dividing regions ( Figure 5Ia ) . However, with increasing copper exposure, cytoplasmic mTOR intensity progressively declined ( Figure 5Ib-f ) . Interestingly, and in contrast to canonical mTOR localization, we observed a consistent and copper dose-dependent nuclear accumulation of mTOR, as visualized in high-resolution optical sections and confirmed in supplementary data (Supplementary Figure S2) . This movement of mTOR into the nucleus might indicate a different role for mTOR in managing stress-related gene activity or changes in DNA structure, which has been suggested in animals but not yet studied in plants 47 . Line profile analysis across nuclear boundaries further validated the spatial redistribution of mTOR from cytoplasm to nucleus under stress ( Figure 5II-V ) . Taken together, these findings suggest that copper-induced oxidative stress activates AMPK and suppresses mTOR-mediated anabolic signaling 46 . Additionally, the surprising presence of mTOR in the nucleus during stress suggests it might play a role in controlling gene activity or changes in gene expression, possibly connecting how the cell responds to stress with its energy use. These results show that the AMPK–mTOR pathway is a key connection between oxidative stress, energy problems, and changes in the cell’s nucleus during heavy metal toxicity. Download figure Open in new tab Figure 5. Copper stress reduces mTOR expression and mitochondrial integrity in tomato root apex cells. (I) Confocal images show MTG (green) and mTOR (red) under increasing copper concentrations. Control cells show strong cytoplasmic mTOR and intact mitochondria; copper stress causes reduced mTOR signal and mitochondrial fragmentation. (II–III) Box plots show a dose-dependent decline in mTOR and MTG intensity. (IV–V) Line profiles confirm spatial reduction in mTOR and mitochondrial signal with increasing copper levels. Scale bars: 50□µm. Data represent mean ± SEM, n = 10 root tips. After activating AMPK and reducing mTOR due to copper stress, we looked at autophagosomes formation as we already see that the mitochondria getting damaged or dysfunctioned. Lysotracker Red (LTR) staining revealed a progressive increase in lysosomal activity in tomato root apex cells with increasing copper concentrations (Supplementary Figure 3) 31 . In control cells, lysosomes appeared small and sparsely distributed, while copper treatment led to enlarged, intensely labeled vesicles localized near fragmented mitochondria, suggesting mitophagy induction ( Supplementary Figure 3 Ia-f) . Intensity profile analysis confirmed lysosomal intensity increases with increase in copper concentration especially under moderate copper levels (Supplementary Figure 3 II) . These changes occurred downstream of AMPK activation, consistent with mTOR inhibition relieving autophagic suppression. However, when there is too much copper, lysosomes group together too much, which might mean they are overwhelmed or stressed, possibly leading to problems with the nucleus and changes in the structure of DNA that are noticed later on. Collectively, these findings indicate that lysosomes initially mitigate damage, but under prolonged stress, they may become dysfunctional, shifting the balance from survival to programmed cell death. 4. mTOR–NRF2 Signaling Orchestrates Peripheral Chromatin Re-Arrangement and Progressive Condensation under Copper Stress Copper-driven oxidative and metabolic stress culminated in pronounced reorganization of nuclear architecture using DAPI and Hoechst (Supplementary Figure 4) in tomato root apex cells ( Figure 6 ) 36 . High-resolution DAPI images show that nuclei in control roots are large, evenly stained, and euchromatin-rich ( Figure 6Ia ) . With increasing copper, nuclei first adopt a “ring-like” pattern in which chromatin relocates to the nuclear periphery while the central region appears partially cleared ( Figure 4Ib ) 48 . Quantification confirmed a progressive decline in nuclear cross-sectional area and intensity of the nucleus ( Figure 6 II-III ) . Centre of mass analyses reveal that peripheral chromatin density rises first, followed by a global spike in total chromatin signal once full condensation is reached ( Figure 6 IV ) . Download figure Open in new tab Figure 6. Copper stress induces nuclear arrangement and displacement in tomato root apex cells. (I) Confocal images of DAPI-stained nuclei show progressive chromatin condensation and nuclear shrinkage under increasing copper concentrations, with control cells displaying large, round euchromatic nuclei. (II–III) Quantification shows reduced DAPI intensity and nuclear area with rising copper, indicating chromatin compaction. (IV) Centre of mass analysis reveals displacement of nuclear position, suggesting spatial reorganization under stress. Scale bars: 50□µm and 2□µm. Data are mean ± SEM, n = 10 root tips. These structural changes coincide spatiotemporally with the nuclear accumulation of both mTOR and NRF2 (shown in Figures 5 – 6 and Supplementary S2) , two factors known to recruit or modulate histone-modifying enzymes. Stress-activated mTOR has been found to work with chromatin remodellers, while nuclear NRF2 helps activate antioxidant genes by changing how easily nucleosomes can be accessed 49 . Their simultaneous presence in the nucleus under copper stress plausibly drives the observed transition, initial peripheral tethering of chromatin (a reversible, gene-regulatory stage) followed by irreversible global compaction when cellular recovery fails. Thus, the nucleus is not merely a passive casualty, it actively remodels its chromatin landscape in response to converging metabolic (mTOR) and redox (NRF2) cues, ultimately locking the cell into a condensed, transcriptionally silent state that precedes programmed cell death. 5. Chromatin Condensation Leads to Terminal Commitment to Cell Death To study how chromatin changes during stress from copper, we used a technique called immunostaining to look for H3K4me3, a marker that shows active gene areas in the chromatin 35 . In control tomato root apex cells, the H3K4me3 signal was evenly distributed throughout the nucleus and chromatin are thread like, indicating a transcriptionally permissive chromatin state and no condensation ( Figure 7 Ia ) 50 , 51 . With increasing copper concentrations, the H3K4me3 signal shifted toward the nuclear periphery, forming ring-like patterns and chromatin is condensed to the periphery, as we see the intensity of the chromatin was higher at periphery ( Figure 7 Ib--e ) . At higher copper doses, this peripheral localization gave way to strong nuclear compaction, reflecting the collapse of euchromatic architecture and it comes again in the centre ( Figure 7 If ) . We quantitatively assessed these chromatin changes by measuring the domain number and cross-sectional area using fluorescence intensity plots and eccentricity ( Figure 7 II-IV ) . The number of domains and the area they cover showed that the chromatin moved to the edges, and the eccentricity indicated a loss of euchromatin features, which matches with reduced gene activity. Download figure Open in new tab Figure 7. Copper stress promotes euchromatin compaction and cell death activation in tomato root apex cells. (I) SRRF super-resolution images of H3K4me3 staining reveal a decline in euchromatin domain number and area with increasing copper. (II–IV) Quantification shows a decrease in euchromatin domain number, area, and an increase in domain eccentricity, indicating chromatin compaction. (V) Confocal images of PI staining show dose-dependent increases in membrane-compromised cells and acidic vesicles. (VI) PI fluorescence intensity increases significantly at 250□µM, suggesting cell death. Scale bars: 2□µm (I), 50□µm (V). Data represent mean ± SEM, n = 10 root tips. To see how much cell death happened due to copper stress, we used propidium iodide (PI) staining on tomato root tip cells 38 . In the control samples, the PI signal was almost not seen, which means the plasma membranes were intact and the cells were alive ( Figure 7 Va ) . However, with increasing copper concentrations, a progressive and region-specific accumulation of PI signals was observed, particularly in the elongation and differentiation zones of the root apex ( Figure 7 Vb-d ) . At higher copper doses, the PI signal became intense and widespread, indicating extensive loss of membrane integrity, a definitive marker of late-stage cell death ( Figure 7 Ve-f ) 52 . The PI-positive staining shows a step-by-step process of early and late cell death, which matches earlier findings of mitochondrial cytochrome c release and chromatin condensation. Fluorescence demonstrated spatial correlation between PI-positive cells and nuclear collapse, confirming that these death signals originate from stress-compromised regions ( Figure 7 VI ) . These findings demonstrate that copper exposure compromises membrane integrity and triggers irreversible cell death once the cell surpasses its compensatory thresholds. This evidence supports the conclusion that cell death under copper stress is a downstream consequence of mitochondrial collapse, oxidative damage, and nuclear disintegration. 6. Shoots Exhibit Delayed Chloroplast and Nuclear Alterations Compared to Roots As this data demonstrates that copper toxicity affects the shoot and root systems differently in tomato plants. In the shoot, chloroplast autofluorescence remains largely intact at lower Cu 2 □ concentrations (≤100□µM), indicating minimal structural disruption 53 . However, at higher concentrations (≥250□µM), chloroplast morphology becomes irregular and signal intensity decreases, reflecting functional impairment. The co-staining with LysoTracker Red (LTR) shows increasing lysosomal activity and autophagy, confirmed by colocalization in the merged images ( Figure 8I-III ) 31 . Download figure Open in new tab Figure 8. Copper-induced chloroplast and nuclear alterations in tomato root and shoot tissues. (I) UV-vis spectra and bar graph showing pigment reduction with increasing Cu 2 □ concentrations. (II-III) Confocal images of shoot cells stained with LTR (red) and chloroplast autofluorescence (green) reveal intact chloroplasts at low Cu 2 □ levels but disruption at higher doses induce autophagy, as seen in colocalization graph. (IV) Shoot cells show chloroplast-nucleus association. Scale bars: 50□µm and 20□µm. Data are mean ± SEM, n = 10 root tips. Despite these changes, the nuclear morphology in shoot cells remains relatively preserved, with nuclei maintaining a central position and showing no significant condensation or peripheral chromatin shift 54 . This contrasts sharply with the root system, where nuclei exhibit shrinkage, lobulation, and chromatin margination even at moderate Cu 2 □ levels 51 . These differences suggest that root cells are more severely and earlier affected by copper stress, likely due to their direct contact with the copper-rich growth medium ( Figure 8 IV ) . Additionally, chloroplast–nucleus association observed in shoot cells may indicate early stress signaling or protective interactions, though without the pronounced nuclear reorganization seen in roots. Overall, the data presented in Figure 8 support the conclusion that roots are more prone to copper-induced damage, while shoot tissues respond more gradually and maintain compartmental integrity under similar conditions. Discussions Copper toxicity in plants often arises from excessive copper in soil, primarily due to industrial waste, mining activities, and overuse of copper-based fertilizers and pesticides. This leads to the accumulation of free Cu 2 □ ions in plant tissues, causing oxidative stress, organelle damage, enzyme inactivation, and disruption of nutrient balance ultimately impairing plant growth and development. This study provides a detailed look at how copper toxicity affects different parts of the cell in Solanum lycopersicum , showing a series of problems with cell structures, stress responses, changes in DNA packaging, and programmed cell death. Our results indicate that mitochondria are the earliest sensors of copper stress, exhibiting fragmentation, membrane depolarization, and cytochrome c release, hallmarks of intrinsic apoptotic signaling 18 , 27 . This mitochondrial collapse leads to a secondary surge in reactive oxygen species (ROS), which contributes to oxidative damage and serves as a signaling cue for downstream regulatory responses 42 . One important discovery from this study is that NRF2 moves into the nucleus and AMPK gets activated, showing a link between redox and energy stress signals 49 . Unexpectedly, we also observed a non-canonical nuclear localization of mTOR under high copper conditions, suggesting potential involvement in chromatin regulation. These signaling events collectively primed the nucleus for structural reorganization. High-resolution DAPI and H3K4me3 imaging revealed a progressive shift from euchromatin-rich, transcriptionally active nuclei to highly condensed, transcribed silent chromatin states. The initial buildup of chromatin at the edges, followed by overall tightening, shows a step-by-step response of the nucleus to stress that is closely connected to metabolism and redox signaling. However, under sustained copper exposure, excessive lysosomal activity may contribute to nuclear destabilization and eventual cell death 55 . Propidium iodide staining showed that the cell membranes broke down in the later stages, leading to cell death, which matched areas where the genetic material fell apart and the mitochondria stopped working 52 . Taken together, our data reveal that the nucleus acts not merely as a passive target but as an active integrator of organelle-derived stress. The sequential activation of the mitochondria-ROS-AMPK/mTOR-NRF2 chromatin axis under copper toxicity establishes a molecular framework for understanding how environmental stress culminates in programmed cell death. Importantly, the identification of nuclear mTOR localization and chromatin reorganization as early stress markers enables the development of targeted strategies to enhance metal stress tolerance in plants ( Figure 9 ) . Download figure Open in new tab Figure 9. Copper-induced cellular stress in plant roots. Under normal conditions (left), cellular pathways remain inactive with no ROS or Cyt C release. Under copper toxicity (right), excess Cu 2 □ from industrial and agricultural sources triggers ROS production, Cyt C release, AMPK activation, and Nrf2 translocation, ultimately leading to cell death. We observed that the root tissues were more susceptible to copper-induced stress compared to the shoots. At lower copper concentrations, the shoot cells did not exhibit significant alterations in chloroplast or nuclear dynamics. However, at higher concentrations, both organelles showed noticeable stress responses, indicating that shoots require a higher threshold of copper exposure to exhibit subcellular damage. This suggests a differential sensitivity between root and shoot tissues, with the root acting as the primary site of copper toxicity. This study provides detailed strategies for metal detoxification in plants using multiple complementary approaches, including physiological analysis, organelle-specific imaging, and stress pathway modulation to understand and mitigate copper-induced toxicity. Conclusion This study reveals that copper toxicity in Solanum lycopersicum triggers a highly coordinated cascade of organelle dysfunction, redox imbalance, and nuclear remodeling. Mitochondria emerge as the primary sensors of Cu-induced stress, undergoing early membrane depolarization and cytochrome c release. This initiates ROS accumulation and the activation of stress-responsive pathways, notably AMPK and NRF2. We identify a novel nuclear localization of mTOR under copper stress, suggesting its potential role in chromatin dynamics. High-resolution chromatin imaging showed a progressive peripheral relocation and condensation of chromatin, coinciding with transcriptional repression and cell death. These nuclear changes are not passive but actively integrate organelle-derived signals, particularly those related to energy and redox status. Lysosomal activation initially supports cellular survival but becomes overwhelmed under high Cu stress, contributing to nuclear destabilization and apoptosis. Together, these findings provide a mechanistic model for copper-induced programmed cell death, mediated through a mitochondrion–ROS–AMPK/mTOR–NRF2–chromatin axis. Importantly, nuclear architecture and chromatin organization emerge as early and sensitive markers of heavy metal stress, offering potential targets for genetic or chemical interventions aimed at improving plant resilience to environmental contaminants. Data and Materials Availability Most of the data we provided in the main manuscript are available with the manuscript itself and its supplementary information. Author Contributions SC and SHC jointly designed and conceptualized the experiments with input from CKN. SC optimized the protocols and performed all plant experiments, imaging and result analysis. SHC contributed to all experimental procedures, and result analysis. AS assisted with imaging. SC and SHC wrote the manuscript with guidance from CKN. CKN supervised and provided overall direction for the project. Ethical and Consent Ethical approval was not required for this study, as it involved standard physiological experiments on Solanum lycopersicum (tomato) root apex cells under copper-induced stress conditions. No genetically modified organisms (GMOs), gene editing, or transgenic lines were used. The experimental procedures complied with institutional and national guidelines for research involving plants. Acknowledgements The authors thank the Advanced Materials Research Centre (AMRC) and Indian Institute of Technology Mandi (IIT Mandi) for providing the facilities and the sophisticated instruments. All the contributing authors thank the Ministry of Education (MoE), India, for the research scholarship. References (1). ↵ Ravet , K. ; Pilon , M. Copper and Iron Homeostasis in Plants: The Challenges of Oxidative Stress . Antioxid Redox Signal 2013 , 19 ( 9 ), 919 . OpenUrl CrossRef PubMed Web of Science (2). ↵ Li , Y. ; Shi , S. ; Zhang , Y. ; Zhang , A. ; Wang , Z. ; Yang , Y. Copper Stress-Induced Phytotoxicity Associated with Photosynthetic Characteristics and Lignin Metabolism in Wheat Seedlings . Ecotoxicol Environ Saf 2023 , 254 , 114739 OpenUrl PubMed (3). Adrees , M. ; Ali , S. ; Rizwan , M. ; Ibrahim , M. ; Abbas , F. ; Farid , M. ; Zia-ur-Rehman , M. ; Irshad , M. K. ; Bharwana , S. A. The Effect of Excess Copper on Growth and Physiology of Important Food Crops: A Review . Environmental Science and Pollution Research 2015 , 22 ( 11 ), 8148 – 8162 . OpenUrl PubMed (4). Gong , Q. ; Li , Z. hua ; Wang , L. ; Zhou , J. yi ; Kang , Q. ; Niu, D. dan . Gibberellic Acid Application on Biomass, Oxidative Stress Response, and Photosynthesis in Spinach (Spinacia Oleracea L.) Seedlings under Copper Stress . Environmental Science and Pollution Research 2021 , 28 ( 38 ), 53594 – 53604 . OpenUrl (5). ↵ Chen , G. ; Li , J. ; Han , H. ; Du , R. ; Wang , X. Physiological and Molecular Mechanisms of Plant Responses to Copper Stress . Int J Mol Sci 2022 , 23 ( 21 ), 12950 . OpenUrl CrossRef PubMed (6). ↵ Shahbaz , M. ; Ravet , K. ; Peers , G. ; Pilon , M. Prioritization of Copper for the Use in Photosynthetic Electron Transport in Developing Leaves of Hybrid Poplar . Front Plant Sci 2015 , 6 (June), 140540 . OpenUrl (7). Weigel , M. ; Varotto , C. ; Pesaresi , P. ; Finazzi , G. ; Rappaport , F. ; Salamini , F. ; Leister , D. Plastocyanin Is Indispensable for Photosynthetic Electron Flow in Arabidopsis Thaliana . Journal of Biological Chemistry 2003 , 278 ( 33 ), 31286 – 31289 . OpenUrl Abstract / FREE Full Text (8). ↵ Cohu , C. M. ; Pilon , M. Cell Biology of Copper . Plant Cell Monographs 2010 , 17 , 55 – 74 . OpenUrl (9). ↵ Reactive oxygen species (ROS) induced oxidative damage to lipids,… | Download Scientific Diagram . (10). ↵ Shabbir , Z. ; Sardar , A. ; Shabbir , A. ; Abbas , G. ; Shamshad , S. ; Khalid , S. ; Natasha Murtaza , G. ; Dumat , C. ; Shahid , M. Copper Uptake, Essentiality, Toxicity, Detoxification and Risk Assessment in Soil-Plant Environment . Chemosphere 2020 , 259 , 127436 . OpenUrl CrossRef PubMed (11). ↵ Shabbir , Z. ; Sardar , A. ; Shabbir , A. ; Abbas , G. ; Shamshad , S. ; Khalid , S. ; Natasha; Murtaza , G.; Dumat , C. ; Shahid , M. Copper Uptake, Essentiality, Toxicity, Detoxification and Risk Assessment in Soil-Plant Environment . Chemosphere 2020 , 259 , 127436 . OpenUrl CrossRef PubMed (12). Wairich , A. ; De Conti , L. ; Lamb , T. I. ; Keil , R. ; Neves , L. O. ; Brunetto , G. ; Sperotto , R. A. ; Ricachenevsky , F. K. Throwing Copper Around: How Plants Control Uptake, Distribution, and Accumulation of Copper . Agronomy 2022, Vol. 12, Page 994 2022 , 12 ( 5 ), 994 . OpenUrl (13). ↵ Cambrollé , J. ; García , J. L. ; Ocete , R. ; Figueroa , M. E. ; Cantos , M. Growth and Photosynthetic Responses to Copper in Wild Grapevine . Chemosphere 2013 , 93 ( 2 ), 294 – 301 . OpenUrl PubMed (14). ↵ Afzal , S. ; Abdul Manap , A. S. ; Attiq , A. ; Albokhadaim , I. ; Kandeel , M. ; Alhojaily , S. M. From Imbalance to Impairment: The Central Role of Reactive Oxygen Species in Oxidative Stress-Induced Disorders and Therapeutic Exploration . Front Pharmacol 2023 , 14 , 1269581 . OpenUrl PubMed (15). ↵ Srivastava , S. ; Mishra , S. ; Tripathi , R. D. ; Dwivedi , S. ; Gupta , D. K. Copper-Induced Oxidative Stress and Responses of Antioxidants and Phytochelatins in Hydrilla Verticillata (L.f.) Royle . Aquatic Toxicology 2006 , 80 ( 4 ), 405 – 415 . OpenUrl CrossRef PubMed Web of Science (16). ↵ Wang , W. ; Sung , S. Chromatin Sensing: Integration of Environmental Signals to Reprogram Plant Development through Chromatin Regulators . J Exp Bot 2024 , 75 ( 14 ), 4332 . OpenUrl PubMed (17). ↵ Kim , J. M. ; Sasaki , T. ; Ueda , M. ; Sako , K. ; Seki , M. Chromatin Changes in Response to Drought, Salinity, Heat, and Cold Stresses in Plants . Front Plant Sci 2015 , 6 ( MAR ), 124925 . OpenUrl (18). ↵ Garcia , L. ; Welchen , E. ; Gonzalez , D. H. Mitochondria and Copper Homeostasis in Plants . Mitochondrion 2014 , 19 ( PB ), 269 – 274 . OpenUrl PubMed (19). ↵ Ezaki , B. ; Higashi , A. ; Nanba , N. ; Nishiuchi , T. An S-Adenosyl Methionine Synthetase (SAMS) Gene from Andropogon Virginicus L. Confers Aluminum Stress Tolerance and Facilitates Epigenetic Gene Regulation in Arabidopsis Thaliana . Front Plant Sci 2016 , 7 (November 2016), 205988 . OpenUrl (20). ↵ Martinez-Zamudio , R. ; Ha , H. C. Environmental Epigenetics in Metal Exposure . Epigenetics 2011 , 6 ( 7 ), 820 . OpenUrl CrossRef PubMed Web of Science (21). ↵ Wairich , A. ; De Conti , L. ; Lamb , T. I. ; Keil , R. ; Neves , L. O. ; Brunetto , G. ; Sperotto , R. A. ; Ricachenevsky , F. K. Throwing Copper Around: How Plants Control Uptake, Distribution, and Accumulation of Copper . Agronomy 2022, Vol. 12, Page 994 2022 , 12 ( 5 ), 994 . OpenUrl (22). ↵ Bhadouriya , S. L. ; Mehrotra , S. ; Basantani , M. K. ; Loake , G. J. ; Mehrotra , R. Role of Chromatin Architecture in Plant Stress Responses: An Update . Front Plant Sci 2021 , 11 , 603380 . doi: 10.3389/FPLS.2020.603380 . OpenUrl CrossRef PubMed (23). ↵ Goldstein , J. I. ; Newbury , D. E. ; Michael , J. R. ; Ritchie , N. W. M. ; Scott , J. H. J. ; Joy , D. C. High Resolution Imaging . Scanning Electron Microscopy and X-Ray Microanalysis 2018 , 147 – 164 . (24). ↵ Salsman , J. ; Dellaire , G. Super-Resolution Radial Fluctuations (SRRF) Microscopy . Methods in Molecular Biology 2022 , 2440 , 225 – 251 . OpenUrl PubMed (25). ↵ Gwinn , D. M. ; Shaw , R. J. AMPK Control of MTOR Signaling and Growth . Enzymes (Essen) 2010 , 28 ( C ), 49 – 75 . OpenUrl (26). Davinelli , S. ; Medoro , A. ; Siracusano , M. ; Savino , R. ; Saso , L. ; Scapagnini , G. ; Mazzone , L. Oxidative Stress Response and NRF2 Signaling Pathway in Autism Spectrum Disorder . Redox Biol 2025 , 83 , 103661 . OpenUrl PubMed (27). ↵ Heiskanen , K. M. ; Bhat , M. B. ; Wang , H. W. ; Ma , J. ; Nieminen , A. L. Mitochondrial Depolarization Accompanies Cytochrome c Release during Apoptosis in PC6 Cells . Journal of Biological Chemistry 1999 , 274 ( 9 ), 5654 – 5658 . OpenUrl Abstract / FREE Full Text (28). ↵ Presley , A. D. ; Fuller , K. M. ; Arriaga , E. A. MitoTracker Green Labeling of Mitochondrial Proteins and Their Subsequent Analysis by Capillary Electrophoresis with Laser-Induced Fluorescence Detection . J Chromatogr B Analyt Technol Biomed Life Sci 2003 , 793 ( 1 ), 141 – 150 . OpenUrl CrossRef PubMed Web of Science (29). ↵ Fu , B. ; Xue , W. ; Zhang , H. ; Zhang , R. ; Feldman , K. ; Zhao , Q. ; Zhang , S. ; Shi , L. ; Pavani , K. C. ; Nian , W. ; Lin , X. ; Wu , H. Microrna-325-3p Facilitates Immune Escape of Mycobacterium Tuberculosis through Targeting Lnx1 via Nek6 Accumulation to Promote Anti-Apoptotic Stat3 Signaling . mBio 2020 , 11 ( 3 ). (30). ↵ Madesh , M. ; Hajnóczky , G. VDAC-Dependent Permeabilization of the Outer Mitochondrial Membrane by Superoxide Induces Rapid and Massive Cytochrome c Release . Journal of Cell Biology 2001 , 155 ( 6 ), 1003 – 1015 . OpenUrl Abstract / FREE Full Text (31). ↵ Zhitomirsky , B. ; Farber , H. ; Assaraf , Y. G. LysoTracker and MitoTracker Red Are Transport Substrates of PLglycoprotein: Implications for Anticancer Drug Design Evading Multidrug Resistance . J Cell Mol Med 2018 , 22 ( 4 ), 2131 . OpenUrl CrossRef PubMed (32). ↵ Zhao , G. ; Forn-Cuní , G. ; Scheers , M. ; Lindenbergh , P. P. ; Yin , J. ; van Loosen , Q. ; Passarini , L. ; Chen , L. ; Snaar-Jagalska , B. E. Simultaneous Targeting of AMPK and MTOR Is a Novel Therapeutic Strategy against Prostate Cancer . Cancer Lett 2024 , 587 , 216657 . OpenUrl PubMed (33). ↵ Immunohistochemical staining of Nrf2 in human endothelial cells . Cells… | Download Scientific Diagram . (34). ↵ Zhao , X. ; Zhu , G. ; Xue , M. ; He , H. Identification and Regulation of EMT Cells in Vivo by Laser Stimulation . APL Bioeng 2025 , 9 ( 2 ), 26119 . OpenUrl (35). ↵ Benayoun , B. A. ; Pollina , E. A. ; Ucar , D. ; Mahmoudi , S. ; Karra , K. ; Wong , E. D. ; Devarajan , K. ; Daugherty , A. C. ; Kundaje , A. B. ; Mancini , E. ; Hitz , B. C. ; Gupta , R. ; Rando , T. A. ; Baker , J. C. ; Snyder , M. P. ; Cherry , J. M. ; Brunet , A. H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency . Cell 2014 , 158 ( 3 ), 673 . OpenUrl CrossRef PubMed Web of Science (36). ↵ Portugal , J. ; Waring , M. J. Assignment of DNA Binding Sites for 4′,6-Diamidine-2-Phenylindole and Bisbenzimide (Hoechst 33258). A Comparative Footprinting Study . BBA -Gene Structure and Expression 1988 , 949 ( 2 ), 158 – 168 . OpenUrl (37). ↵ H3K4me3 immunostaining in the porcine nonsexed E6 blastocyst including… | Download Scientific Diagram . (38). ↵ Rosenberg , M. ; Azevedo , N. F. ; Ivask , A. Propidium Iodide Staining Underestimates Viability of Adherent Bacterial Cells . Scientific Reports 2019 9:1 2019 , 9 ( 1 ), 1 – 12 . OpenUrl PubMed (39). ↵ Chen , G. ; Li , J. ; Han , H. ; Du , R. ; Wang , X. Physiological and Molecular Mechanisms of Plant Responses to Copper Stress . Int J Mol Sci 2022 , 23 ( 21 ), 12950 . OpenUrl CrossRef PubMed (40). ↵ Ruiz , L. M. ; Libedinsky , A. ; Elorza , A. A. Role of Copper on Mitochondrial Function and Metabolism . Front Mol Biosci 2021 , 8 , 711227 . OpenUrl PubMed (41). ↵ Rius-Pérez , S. ; Pérez , S. ; Toledano , M. B. ; Sastre , J. Mitochondrial Reactive Oxygen Species and Lytic Programmed Cell Death in Acute Inflammation . Antioxid Redox Signal 2023 , 39 ( 10–12 ), 708 . OpenUrl PubMed (42). ↵ Addabbo , F. ; Montagnani , M. ; Goligorsky , M. S. Mitochondria and Reactive Oxygen Species . Hypertension 2009 , 53 ( 6 ), 885 . OpenUrl CrossRef PubMed (43). ↵ Kim , K. H. ; Lee , C. B. Socialized Mitochondria: Mitonuclear Crosstalk in Stress . Experimental & Molecular Medicine 2024 56:5 2024 , 56 ( 5 ), 1033 – 1042 . OpenUrl PubMed (44). ↵ Ngo , V. ; Duennwald , M. L. Nrf2 and Oxidative Stress: A General Overview of Mechanisms and Implications in Human Disease . Antioxidants 2022 , 11 ( 12 ), 2345 . OpenUrl PubMed (45). ↵ Lin , J. ; Wang , L. ; Huang , M. ; Xu , G. ; Yang , M. Metabolic Changes Induced by Heavy Metal Copper Exposure in Human Ovarian Granulosa Cells . Ecotoxicol Environ Saf 2024 , 285 , 117078 . OpenUrl PubMed (46). ↵ Gleason , C. E. ; Lu , D. ; Witters , L. A. ; Newgard , C. B. ; Birnbaum , M. J. The Role of AMPK and MTOR in Nutrient Sensing in Pancreatic β-Cells . Journal of Biological Chemistry 2007 , 282 ( 14 ), 10341 – 10351 . OpenUrl Abstract / FREE Full Text (47). ↵ Zhao , T. ; Fan , J. ; Abu-Zaid , A. ; Burley , S. K. ; Zheng , X. F. S. Nuclear MTOR Signaling Orchestrates Transcriptional Programs Underlying Cellular Growth and Metabolism . Cells 2024, Vol. 13, Page 781 2024 , 13 ( 9 ), 781 . OpenUrl (48). ↵ Amiad-Pavlov , D. ; Lorber , D. ; Bajpai , G. ; Reuveny , A. ; Roncato , F. ; Alon , R. ; Safran , S. ; Volk , T. Live Imaging of Chromatin Distribution Reveals Novel Principles of Nuclear Architecture and Chromatin Compartmentalization . Sci Adv 2021 , 7 ( 23 ), eabf6251 . OpenUrl FREE Full Text (49). ↵ Ngo , V. ; Duennwald , M. L. Nrf2 and Oxidative Stress: A General Overview of Mechanisms and Implications in Human Disease . Antioxidants 2022 , 11 ( 12 ), 2345 . OpenUrl PubMed (50). ↵ Luo , L. ; Gassman , K. L. ; Petell , L. M. ; Wilson , C. L. ; Bewersdorf , J. ; Shopland , L. S. The Nuclear Periphery of Embryonic Stem Cells Is a Transcriptionally Permissive and Repressive Compartment . J Cell Sci 2009 , 122 ( 20 ), 3729 . OpenUrl Abstract / FREE Full Text (51). ↵ Probst , A. V. ; Mittelsten Scheid , O. Stress-Induced Structural Changes in Plant Chromatin . Curr Opin Plant Biol 2015 , 27 , 8 – 16 . OpenUrl CrossRef PubMed (52). ↵ Zhang , Y. ; Chen , X. ; Gueydan , C. ; Han , J. Plasma Membrane Changes during Programmed Cell Deaths . Cell Res 2018 , 28 ( 1 ), 9 – 21 . OpenUrl CrossRef PubMed (53). ↵ Brunkard , J. O. ; Runkel , A. M. ; Zambryski , P. C. Chloroplasts Extend Stromules Independently and in Response to Internal Redox Signals . Proc Natl Acad Sci U S A 2015 , 112 ( 32 ), 10044 – 10049 . OpenUrl Abstract / FREE Full Text (54). ↵ Libault , M. ; Evans , D. E. ; Groves , N. R. ; Tamura , K. ; Goto , C. ; Hara-Nishimura , I. Regulation and Physiological Significance of the Nuclear Shape in Plants . Front Plant Sci 2021 , 12 , 673905 . OpenUrl PubMed (55). ↵ Berg , A. L. ; Rowson-Hodel , A. ; Wheeler , M. R. ; Hu , M. ; Free , S. R. ; Kermit L. Carraway, I. Engaging the Lysosome and Lysosome-Dependent Cell Death in Cancer . Breast Cancer 2022 , 195 – 230 . View the discussion thread. Back to top Previous Next Posted July 21, 2025. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Copper Stress Trigger Organelles Communication and Chromatin Condensation Leading to Cell Death in Solanum lycopersicum Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Copper Stress Trigger Organelles Communication and Chromatin Condensation Leading to Cell Death in Solanum lycopersicum Sakshi Chouhan , Shilpa Chandra , Abdul Salam , Chayan Kanti Nandi bioRxiv 2025.07.17.665307; doi: https://doi.org/10.1101/2025.07.17.665307 Share This Article: Copy Citation Tools Copper Stress Trigger Organelles Communication and Chromatin Condensation Leading to Cell Death in Solanum lycopersicum Sakshi Chouhan , Shilpa Chandra , Abdul Salam , Chayan Kanti Nandi bioRxiv 2025.07.17.665307; doi: https://doi.org/10.1101/2025.07.17.665307 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Plant Biology Subject Areas All Articles Animal Behavior and Cognition (7633) Biochemistry (17681) Bioengineering (13890) Bioinformatics (41930) Biophysics (21446) Cancer Biology (18586) Cell Biology (25493) Clinical Trials (138) Developmental Biology (13374) Ecology (19897) Epidemiology (2067) Evolutionary Biology (24308) Genetics (15607) Genomics (22498) Immunology (17736) Microbiology (40385) Molecular Biology (17175) Neuroscience (88584) Paleontology (666) Pathology (2831) Pharmacology and Toxicology (4823) Physiology (7641) Plant Biology (15149) Scientific Communication and Education (2045) Synthetic Biology (4293) Systems Biology (9823) Zoology (2271)