Biology subjects

Nunes-Nesi, A.

Publications and source records attributed to Nunes-Nesi, A..

7 recordsLinked to original sources

bioRxiv2026

Lysine biosynthesis impairment shapes heat-stress acclimation through metabolic and transcriptional reprogramming in Arabidopsis thaliana

Global warming is increasing the frequency and intensity of high-temperature episodes, limiting plant productivity. However, the molecular mechanisms integrating primary metabolism with the heat stress response remains poorly understood. Here, we show that lysine biosynthesis contributes to the coordination of physiological, metabolic and transcriptional responses to heat stress in Arabidopsis thaliana. We compared wild-type, the lysine-biosynthesis mutant dapat, and the salicylic acid (SA)-biosynthesis and signaling mutants sid2-1 and npr1-3 under prolonged warming (6C above control for 7 days) and heat shock (38C for 6 h), followed by recovery. We assessed growth, gas exchange, photosynthetic performance, free SA, salicylic acid glucoside (SAG), salicylic acid glucose ester (SGE), and total SA content, primary metabolite profiles, heat-stress-responsive gene expression and transcriptome-wide changes by RNA sequencing. Before heat stress, dapat mutant presented a distinct metabolic state, marked by amino-acid accumulation, altered organic-acid profiles, reduced soluble sugars and elevated endogenous SA. This metabolic configuration persisted during prolonged warming, whereas WT and SA-pathway mutants underwent more dynamic reprogramming. Heat shock, by contrast, elicited a more convergent response across genotypes. Despite reduced basal PSII efficiency, dapat maintained photosynthetic performance during prolonged warming and recovered. Its transcriptional response, however, differed from that of WT and SA-pathway mutants: selected heat-responsive genes were constitutively or more strongly expressed, whereas some canonical heat-stress regulators showed weaker induction after heat shock. RNA-seq further revealed a largely conserved core heat-shock response but genotype-dependent regulation of defense, hormone and amino-acid-metabolism programs, particularly during recovery. Together, these findings indicate that impaired DAPAT activity establishes a metabolically primed but energetically constrained state that reshapes gas exchange, photosynthetic acclimation and heat-responsive transcription. Lysine homeostasis therefore emerges as a regulatory node linking primary metabolism and SA accumulation with SA-dependent and SA-independent components of heat-stress acclimation.

plant biology↗

bioRxiv2025

Cell-specific regulation of TCA cycle and cell division related genes at roots following aluminium exposure

Aluminium (Al) toxicity is a critical factor that limits plant growth in acidic soils (pH < 5.5) worldwide. Intracellular Al can bind to various biomolecules and significantly affect gene expression, protein biosynthesis, and cell membrane integrity, ultimately inhibiting nutrients and water uptake. This leads to the arrest of root cell divisions and growth. Organic acids (OAs) produced in mitochondrial-related reactions are strongly linked to Al tolerance, as they bind to Al and neutralize its toxic effects. Recently, the manipulation of root cell divisions through DNA checkpoints has been proposed as an alternative to increase Al tolerance. In this context, molecular interactions between these two mechanisms could potentially enhance plant tolerance to Al toxicity. Here, we investigate this topic using a translatome approach, which enables specific analyses of root cell types (namely, whole root, the quiescent centre region, and the cortical region). This approach offers a promising tool for unravelling how mitochondrial metabolism, particularly the TCA cycle, and the DNA damage response (DDR) pathway are interconnected in Al-mitigation process. Our results revealed that the TCA cycle is induced in differentiated cells, with no significant alteration in meristematic cells, while genes associated with cell cycle progression and DNA checkpoints show differential expression across the distinct cell types. Collectively, our data contribute to understand cell-specific internal detoxification mechanism related to Al tolerance in plants. This knowledge could assist crop breeding by providing a better understanding of the cellular physiological responses to Al toxicity.

plant biology↗

bioRxiv2025

Impaired lysine biosynthesis drives constitutive energy stress priming and darkness stress responses

Plant survival under prolonged darkness relies on dynamic metabolic reprogramming that redirects limited carbon resources toward mitochondrial respiration and nutrient remobilization. Although amino acids function as alternative respiratory substrates during carbon starvation, how their biosynthesis integrates into this metabolic adjustment remains poorly understood. Here, we investigated the role of lysine biosynthesis using the dapat mutant, which exhibits photoperiod-dependent hypersensitivity to extended darkness. Under short-day conditions, dapat plants exhibited accelerated senescence. reduced photosystem II maximum quantum efficiency, pronounced protein degradation, and accumulation of amino acid, ultimately failing to recover after nine days of darkness. By contrast, survival was largely restored under neutral-day conditions, indicating that restricted carbohydrate reserves during short-day growth exacerbate the mutant phenotype. Remarkably, transcript profiling further revealed that reduced DAPAT activity constitutively activates a catabolic program, including genes associated with amino acid degradation, alternative respiratory pathways, senescence, and autophagy, even under non-stress conditions. Together, these findings identify DAPAT-mediated lysine biosynthesis as a central metabolic hub linking carbon availability to energy and stress signaling. Disruption of this pathway compromises metabolic flexibility and limits the capacity to withstand prolonged carbon starvation. Our results provide new insights into how primary metabolism coordinates stress responses to extended darkness and highlight amino acid biosynthesis as an important component of plant resilience under energy-deprived darkness conditions.

plant biology↗

bioRxiv2025

The improved auxin signalling via entire mutation enhances aluminium tolerance in tomato

Acidic soils limit food production in many developing countries by promoting the solubilization of aluminium (Al) cations. Consequently, roots absorb this metal from soil solution, arresting their growth while reducing water and nutrient uptake. To mitigate the impacts of Al, plants rewire their metabolism and growth, with diverse mechanisms in this process shaped by changes in auxin signalling. Here, we present a comprehensive study on the significance of auxin signalling for Al tolerance. We used tomato mutants with reduced (diageotropica, dgt) and increased (entire) auxin sensitivity to assess the regulation of growth and metabolism in plants coping with Al toxicity. Our results indicated a reduced Al tolerance in the dgt mutant, whereas entire was able to tolerate toxic levels of Al. This contrast can be explained by a differential accumulation of reactive oxygen species (ROS) in the root transition zone, where dgt exhibited more differentiated cells, making the pericycle evident. In contrast, entire showed only slight alterations in the transition zone, with root meristematic cells maintaining a reduced level of cell differentiation, which can be associated with sustained growth under toxic Al levels. These differences were followed by alterations in metabolites related to Al sensitivity in the roots of dgt plants, whereas the entire mutant exhibited only slight metabolic changes. Collectively, our results suggest that genetic modifications to regulate auxin perception have the potential to increase Al tolerance in crops.

plant biology↗

bioRxiv2022

The temporal regulation inter-leaves from domesticated-tomato contrasts with timelessness of its wild ancestors

Cells, tissues, and organs are characterized by harbouring complex systems allowing communication between one another. Plant domestication was demonstrated to have structured the circadian rhythms, while also synchronising flowering and metabolism. Here, we demonstrate that the domesticated tomato (Solanum lycopersicum) manifests more synchronized rhythmicity across the whole plant. Consequently, the leaf development program is more coordinated in this species than in its wild relatives, wherein S. lycopersicum young leaves develop slowly in comparison to mature leaves. Young leaves from wild tomatoes display higher photosynthesis than mature leaves, while large metabolite accumulations occur across plant segments. Consequently, the diel metabolite levels are rather similar between young and mature leaves in the wild tomato S. pennellii, whereas the expression patterns for circadian clock genes are widely contrasting between both leaves. We further demonstrated that additions of genes related to domestication into the wild tomato S. pimpinellifolium appear to synchronize the development of young and mature leaves to be rather similar to that observed for S. lycopersicum. Collectively, the strengthening of inter-organs relationships on domesticated tomato indicates a synchronized biology, which is most likely fundamental to explaining its elevated yield.

plant biology↗

bioRxiv2021

Hotter chili peppers by hybridisation: heterosis and reciprocal effects

The selection of pure lines followed by crosses to create superior hybrids is one of the oldest strategies in crop breeding. However, in domesticated species of the Capsicum genus hybrid breeding has lagged, in part due to a lack of detailed information about the phenotypic and metabolic consequences of hybridization. Here, we performed reciprocal crosses between four inbred varieties of two species of cultivated C. chinense (cv. Habanero and Biquinho) and C. annuum var. annuum (cv. Jalapeno and cv. Cascadura Ikeda). These varieties were specifically selected for their highly divergent traits, including plant growth habit, fruit size, shape and pungency: Habanero and Jalapeno peppers are highly pungent forms, particularly popular in Mexico. The Biquinho cultivar of C. chinense and the Cascadura Ikeda bell pepper are traditional sweet cultivars from Brazil. From the parental genotypes and from the progeny of the reciprocal crosses, we measured 28 phenotypic traits, including plant growth, and yield, 32 fruit shape parameters, and 50 fruit pericarp and placenta metabolites, including capsaicinoids. We found large differences for agronomic and metabolic traits between the genotypes, including heterosis for pungency and reciprocal effects for agronomic traits. We also show that the strong association between fruit shape and pungency can be broken in intraspecific hybrids, paving the way for the precision breeding of novel varieties. Once sentence summaryHybrids of Capsicum peppers display heterosis and reciprocal effects for agronomic traits and fruit pungency

plant biology↗

bioRxiv2021

Photoperiod shapes aluminium tolerance in plants

Aluminium is a limiting factor for crop productivity in acidic soils (pH [≤] 5.5). Since acid soil distribution on Earth cannot adequately explain the differential Al tolerance across the plant kingdom, we investigated photoperiod effects on plant Al tolerance. We observed that with increasing distance from the equator, Al tolerance disappears, suggesting a relationship with the photoperiod. Long-day (LD) species are generally more Al-sensitive than short-day (SD) species, whereas genetic conversion of tomato for SD growth boosts Al tolerance. Reduced Al tolerance correlates with DNA-checkpoint activation under LD. DNA-checkpoint-related genes are under positive selection in Arabidopsis accessions from regions with shorter days, suggesting photoperiod acts as a selective barrier for Al tolerance. Our findings revealed that diel regulation and genetic diversity affect Al tolerance, suggesting that day-length orchestrates Al tolerance. One-Sentence SummaryAluminum is a major constraint for crop yield worldwide. We reveal that photoperiod acts as a barrier for Al tolerance in plants.

plant biology↗