Biology subjects

Balazadeh, S.

Publications and source records attributed to Balazadeh, S..

11 recordsLinked to original sources

bioRxiv2025

The plant longevity gene AHL15 delays leaf senescence by repressing ORESARA1 and cytokinin degradation

The Arabidopsis thaliana (Arabidopsis) AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15) gene is associated with various longevity phenotypes and extends the life span of plants when overexpressed. In this study, we show that, in addition to previously described longevity phenotypes, constitutive overexpression of AHL15 in Arabidopsis delays leaf senescence, whereas ahl15 loss-of-function accelerates this process. Dexamethasone-induced nuclear localization of AHL15-GR during dark-triggered senescence results in a stay-green phenotype and represses the expression of several early senescence-associated genes. Among these, the ORESARA1 (ORE1) locus is directly bound by AHL15, suggesting a direct repressive effect of AHL15 on senescence. Furthermore, we demonstrate that AHL15 acts by directly repressing the expression of several CYTOKININ OXIDASE (CKX) genes involved in cytokinin inactivation, resulting in a delayed degradation of cytokinins during dark-induced senescence. Cytokinins are known to delay senescence, and together with the downregulation of ORE1 expression, this explains the repressive effect of AHL15 on senescence. SignificanceHere, we show that in addition to its previously reported effects on aging processes, the AT-HOOK MOTIF NUCLEAR LOCALIZED-family protein AHL15 also represses leaf senescence. Our results demonstrate that AHL15 delays the senescence program in two ways: by directly repressing the senescence master regulator ORESARA1, and by transcriptional repression of CYTOKININ OXIDASE genes, resulting in a delayed breakdown of the senescence-inhibiting hormone cytokinin, which together explain the strong stay-green phenotype of AHL15-overexpressing plants.

plant biology↗

bioRxiv2025

Multi-Omics Analysis of Heat Stress-Induced Memory in Arabidopsis

In their natural environment, plants experience temperature fluctuations, including intensified heat waves driven by climate change, which pose significant threats to their productivity. To adapt, plants have evolved diverse mechanisms to withstand heat stress (HS), minimizing potential damage and ensuring survival. One such adaptation is acquired thermotolerance (AT), where prior exposure to HS primes plants to withstand subsequent severe HS. AT can persist for several days and involves a recovery period during which plants establish heat stress memory (HSM), reorganize cellular processes, and strengthen stress resilience. The molecular mechanisms underlying HSM remain the subject of active investigation. In this study, we employ a high-throughput comparative multi-omics approach to unravel the transcriptome, metabolome, and proteome of Arabidopsis thaliana seedlings during distinct intervals of the HSM phase. Our findings provide insights into the intricacies of HS recovery and the memory process. Notably, distinct temporal responses emerge at both the transcriptional and protein levels during the early and late recovery phases. Transcripts associated with HSM are upregulated during the early HS recovery phase, indicating a rapid response crucial for initial memory formation, while corresponding protein levels remain elevated throughout the recovery period, supporting memory consolidation. Additionally, metabolite profiles reveal distinctive patterns across the HS memory phase. This marks the first detailed multi-omic analysis of the HSM phase in Arabidopsis seedlings, providing insights into the multifaceted nature of this complex process. These comprehensive datasets hold promise in elucidating regulators of HS resilience, thereby enhancing efforts in breeding HS-tolerant crops

plant biology↗

bioRxiv2024

Integrating Gene Expression Analysis and Ecophysiological Responses to Water Deficit in Leaves of Tomato Plants

Soil water deficit (WD) is one of the most important abiotic stresses affecting plant survival and crop yield. Despite its economic relevance, many gaps remain in our understanding of how crops respond to WD, especially concerning the synergistic coordination of molecular and ecophysiological adaptations delaying plant damage and mortality. In this study, we investigated the gene expression imposed by a progressive WD and combined it with measurements pointing to key ecophysiological thresholds in leaves of tomato plants. We uncovered the transcriptomic changes in mature leaves at four stages defined by physiological markers relating to different WD intensities: partial stomatal closure, complete stomatal closure, after leaf wilting, and beginning of embolism development in the veins. By identifying key transcription factors (TFs) across these progressively worsening WD stages, we investigated the timing and impact of ABA-(in)dependent gene regulatory pathways during WD. In addition, we compared the transcriptome in young developing versus mature leaves and explored the physiological mechanisms that may explain the higher tolerance to dehydration in younger leaves. By correlating the transcriptomic changes to precise ecophysiological measurements, the combined dataset will serve as a framework for future studies comparing leaf molecular and physiological responses to WD at specific intensities. HighlightIntegrated ecophysiological and gene expression analyses identify key mechanisms underlying the different thresholds of tomato responses to water deficit

plant biology↗

bioRxiv2022

Ethylene-mediated phosphorylation of ORESARA1 induces sequential leaf death during flooding in Arabidopsis

The volatile phytohormone ethylene is a major regulator of plant adaptive responses to flooding. In flooded plant tissues, it quickly increases to high concentrations due to its low solubility and diffusion rates in water. The passive, quick and consistent accumulation of ethylene in submerged plant tissues makes it a reliable cue to trigger flood-acclimative responses, including metabolic adjustments to cope with flood-induced hypoxia. However, persistent ethylene accumulation also accelerates leaf senescence. Stress-induced senescence hampers the photosynthetic capacity and stress recovery. In submerged Arabidopsis shoots, senescence follows a strict age-dependent pattern starting with the older leaves. Although mechanisms underlying ethylene-mediated senescence have been uncovered, it is unclear how submerged plants avoid an indiscriminate breakdown of leaves despite high systemic ethylene accumulation. Here we demonstrate in Arabidopsis plants that even though submergence triggers a leaf-age independent activation of ethylene signaling via EIN3, senescence was initiated only in the old leaves, and independent of the N-degron pathway of oxygen sensing. This EIN3 stabilization also led to the overall transcript and protein accumulation of the senescence-promoting transcription factor ORESARA1 (ORE1). ORE1 protein accumulated in both old and young leaves during submergence. However, leaf age-dependent senescence could be explained by ORE1 protein activation specifically in old leaves, independent of the previously identified age-dependent control of ORE1 via miR164. Our results unravel a mechanism by which plants regulate the speed and pattern of senescence during environmental stresses like flooding. The age-dependent activity of ORE1 ensures that older expendable leaves are dismantled first, thus prolonging the life of younger leaves and meristematic tissues vital to whole plant survival. Significance statementFlooded plants systemically accumulate saturating concentrations of the senescence promoting volatile hormone ethylene. Yet, leaf senescence follows a strict age-dependent gradient, thus prolonging the survival of young leaves and meristematic tissue. Here we show that in flooded plants, age-independent activation of ethylene signaling via EIN3, induces the systemic accumulation of the senescence-inducing transcription factor ORE1. Premature senescence of younger tissues is prevented by the posttranslational activation of ORE1 specifically in old leaves, where it induces the transcription of senescence-associated genes. Our results highlight how a systemic stress signal (ethylene accumulation upon flooding) induces a signaling cascade that diverges in an age-dependent manner, and eventually leads to an age-dependent physiological output (leaf senescence).

plant biology↗

bioRxiv2021

The diversity of quinoa morphological traits and seed metabolic composition

Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa. O_TBL View this table: org.highwire.dtl.DTLVardef@160e784org.highwire.dtl.DTLVardef@ff8bd1org.highwire.dtl.DTLVardef@13446daorg.highwire.dtl.DTLVardef@11796eeorg.highwire.dtl.DTLVardef@1b607b8_HPS_FORMAT_FIGEXP M_TBL C_TBL

plant biology↗

bioRxiv2021

Dual control of MAPK activities by AP2C1 and MKP1 MAPK phosphatases regulates defence responses in Arabidopsis

Mitogen-activated protein kinase (MAPK) cascades transmit environmental signals and induce stress and defence responses in plants. These signalling cascades are negatively controlled by specific phosphatases of the type 2C Ser/Thr protein phosphatase (PP2C) and dual-specificity phosphatase (DSP) families that inactivate stress-induced MAPKs; however, the interplay between phosphatases of these different types has remained unknown. Our work reveals that different Arabidopsis MAPK phosphatases, the PP2C-type AP2C1 and the DSP-type MKP1, exhibit both specific and overlapping functions in plant stress responses. Each single mutant and ap2c1 mkp1 double mutant displayed enhanced wound-induced activation of MAPKs MPK3, MPK4, and MPK6, as well as induction of a set of transcription factors. Moreover, ap2c1 mkp1 double mutants show an autoimmune-like response, associated with elevated levels the stress hormones salicylic acid and ethylene, and of the phytoalexin camalexin. Interestingly, this phenotype is reduced in ap2c1 mkp1 mpk6 triple mutants, suggesting that the autoimmune-like response is due to MPK6 misregulation. We conclude that the evolutionarily distant MAPK phosphatases AP2C1 and MKP1 contribute crucially to the tight control of MPK6 activity, ensuring appropriately balanced stress signalling and suppression of autoimmune-like responses during plant growth and development. HighlightDouble MAPK phosphatase mutant plants ap2c1 mkp1 exhibit constitutive, autoimmune-like stress responses, dependent on their substrate MAPK MPK6.

plant biology↗

bioRxiv2021

NAC transcription factor RD26 is a regulator of root hair morphogenic plasticity

Root hairs are outgrowths of epidermal cells central for water and nutrient acquisition. Root hair growth is plastically modified by environmental cues. A frequent response to water limitation is active shortening of root hairs, involving largely unknown molecular mechanisms. A root hair-specific cis-regulatory element (RHE) integrates developmental cues with downstream signalling of root hair morphogenesis. Here, we demonstrate NAC transcription factor RD26 to be a key expressional regulator of this drought stress-triggered developmental response in Arabidopsis thaliana. RD26 directly represses RSL4 and RSL1, two master transcription regulators of root hair morphogenesis, by binding RHE. RD26 further represses core cell wall modification genes including expansins (EXPA7, EXPA18), hydroxyproline-rich glycoproteins (LRX1), xyloglucan endotransglucosylases/hydrolases (XTH12, 13, 14, 26), class III peroxidases (PRX44) and plasma membrane H+-ATPase (AHA7) through RHE. Of note, several RD26-repressed genes are activated by RSL4. Thus, by repressing RSL4 and numerous cell wall-related genes, RD26 governs a robust gene regulatory network for restricting root hair growth under drought. A similar regulatory network exists in tomato, indicating evolutionary conservation across species. Significance statementIn plants, root hairs play a vital role for water and nutrient acquisition, soil anchorage, and microbial interactions. During drought stress, root hair growth is suppressed as an adaptive strategy to save cellular energy. We identified NAC transcription factor RD26 as a key regulator of this developmental plasticity in the model plant Arabidopsis thaliana. RD26 directly and negatively controls the transcriptional activity of key root hair developmental genes, RSL1 and RSL4. Furthermore, RD26 suppresses the expression of several functional genes underlying root hair development including numerous cell wall-related genes. RD26 thus governs a robust gene regulatory network underlying the developmental response to drought stress. A similar regulatory network exists in tomato indicating evolutionary conservation of this mechanism across species.

plant biology↗

bioRxiv2021

An HB40 - JUNGBRUNNEN1 - GA 2-OXIDASE regulatory module for gibberellin homeostasis in Arabidopsis

The phytohormones gibberellins (GAs) play fundamental roles in almost every aspect of plant growth and development. Although there is good knowledge about GA biosynthetic and signaling pathways, factors contributing to the mechanisms homeostatically controlling GA levels remain largely unclear. Here, we demonstrate that homeobox transcription factor HB40 of the HD-Zip family in Arabidopsis thaliana regulates GA content at two additive control levels. We show that HB40 expression is induced by GA and in turn reduces the levels of endogenous bioactive GAs by a simultaneous reduction of GA biosynthesis and increased GA deactivation. Hence, HB40 overexpression leads to typical GA-deficiency traits, such as small rosettes, reduced plant height, delayed flowering, and male sterility. In contrast, a loss-of-function hb40 mutation enhances GA-controlled growth. Genome-wide RNA-sequencing combined with molecular-genetic analyses revealed that HB40 directly activates transcription of JUNGBRUNNEN1 (JUB1), a key TF repressing growth by suppressing GA biosynthesis and signaling. HB40 also represses genes encoding GA 2-oxidases (GA2oxs) which are major GA catabolic enzymes. The effect of HB40 is ultimately mediated through induction of nuclear growth-repressing DELLA proteins. Our results thus uncover an important role of the HB40/JUB1/GA2ox/DELLA network in controlling GA homeostasis during plant growth.

plant biology↗

bioRxiv2020

Primary carbohydrate metabolism genes participate in heat stress memory at the shoot apical meristem of Arabidopsis thaliana

Although we have a good understanding of the development of shoot apical meristems (SAM) in higher plants, and the function of the stem cells (SCs) embedded in the SAM, there is surprisingly little known of its molecular responses to abiotic stresses. Here, we show that the SAM of Arabidopsis thaliana senses heat stress (HS) and retains an autonomous molecular memory of a previous non-lethal HS, allowing the SAM to regain growth after exposure to an otherwise lethal HS several days later. Using RNA-seq, we identified genes participating in establishing a SAM-specific HS memory. The genes include HEAT SHOCK TRANSCRIPTION FACTORs (HSFs), of which HSFA2 is essential, but not sufficient, for full HS memory in the SAM, the SC regulators CLAVATA1 (CLV1) and CLV3, and several primary carbohydrate metabolism genes, including FRUCTOSE-BISPHOSPHATE ALDOLASE 6 (FBA6). We found that expression of FBA6 during HS at the SAM complements that of FBA8 in the same organ. Furthermore, we show that sugar availability at the SAM is essential for survival at high-temperature HS. Collectively, plants have evolved a sophisticated protection mechanism to maintain SCs and, hence, their capacity to re-initiate shoot growth after stress release.

plant biology↗

bioRxiv2020

Autophagy is responsible for the accumulation of proteogenic dipeptides in response to heat stress in Arabidopsis thaliana.

Proteogenic dipeptides are intermediates of proteolysis as well as an emerging class of small-molecule regulators with diverse and often dipeptide-specific functions. Herein, prompted by differential accumulation of dipeptides in a high-density Arabidopsis thaliana time-course stress experiment, we decided to pursue an identity of the proteolytic pathway responsible for the buildup of dipeptides under heat conditions. By querying dipeptide accumulation versus available transcript data, autophagy emerged as a top hit. To examine whether autophagy indeed contributes to the accumulation of dipeptides measured in response to heat stress, we characterized the loss-of-function mutants of crucial autophagy proteins to test whether interfering with autophagy would affect dipeptide accumulation in response to the heat treatment. This was indeed the case. This work implicates the involvement of autophagy in the accumulation of proteogenic dipeptides in response to heat stress in Arabidopsis.

biochemistry↗

bioRxiv2018

Tomato fruit ripening factor NOR controls leaf senescence

NAC transcription factors (TFs) are important regulators of expressional reprogramming during plant development, stress responses and leaf senescence. NAC TFs also play important roles in fruit ripening. In tomato (Solanum lycopersicum), one of the best characterized NAC involved in fruit ripening is NON-RIPENING (NOR) and the non-ripening (nor) mutation has been widely used to extend fruit shelf life in elite varieties. Here, we show that NOR additionally controls leaf senescence. Expression of NOR increases with leaf age, and developmental as well as dark-induced senescence are delayed in the nor mutant, while overexpression of NOR promotes leaf senescence. Genes associated with chlorophyll degradation as well as senescence-associated genes (SAGs) show reduced and elevated expression, respectively, in nor mutants and NOR overexpressors. Overexpression of NOR also stimulates leaf senescence in Arabidopsis thaliana. In tomato, NOR supports senescence by directly and positively regulating the expression of several senescence-associated genes including, besides others, SlSAG15 and SlSAG113, SlSGR1 and SlYLS4. Finally, we find that another senescence control NAC TF, namely SlNAP2, acts upstream of NOR to regulate its expression. Our data support a model whereby NAC TFs have often been recruited by higher plants for both, the control of leaf senescence and fruit ripening.

plant biology↗