Biology subjects

Araujo, W. L.

Publications and source records attributed to Araujo, W. L..

11 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↗

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

Deciphering the major metabolic pathways associated with aluminum tolerance in popcorn roots using label-free quantitative proteomics

Aluminum toxicity is one of the most important abiotic stresses that affect crop production worldwide. The soluble form (Al3+) inhibits root growth by altering water and nutrients uptake, which also reduces plant growth and development. Under a long term Al3+ exposure, plants can activate several tolerance mechanisms, and to date, there are no reports of large-scale proteomic data of maize in response to this ion. To investigate the post-transcriptional regulation in response to Al toxicity, we performed a label-free quantitative proteomics for comparative analysis of two Al-contrasting popcorn inbred lines and an Al-tolerant commercial hybrid during 72 h under Al-stress. A total of 489 differentially accumulated proteins (DAPs) were identified in the Al-sensitive inbred line, 491 in the Al-tolerant inbred line, and 277 in the commercial hybrid. Among them, 120 DAPs were co-expressed in both Al tolerant genotypes. Bioinformatics analysis indicated that starch and sucrose metabolism, glycolysis/gluconeogenesis, and carbohydrate metabolism were significant biochemical processes regulated in response to Al toxicity. The up accumulation of sucrose synthase and the increase of sucrose content and starch degradation suggest that these components may enhance popcorn tolerance to Al stress. The up-accumulation of citrate synthase suggests a key role of this enzyme in the detoxification process in the Al-tolerant inbred line. The integration of transcriptomic and proteomic data indicated that the Al tolerance response presents a complex regulatory network into the transcription and translation dynamics of popcorn roots development.

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↗

bioRxiv2020

Autophagy is required for lipid homeostasis during dark-induced senescence in Arabidopsis

Autophagy is an evolutionarily conserved mechanism that mediates the degradation of cytoplasmic components in eukaryotic cells. In plants, autophagy has been extensively associated with the recycling of proteins during carbon starvation conditions. Even though lipids constitute a significant energy reserve, our understanding of the function of autophagy in the management of cell lipid reserves and components remains fragmented. To further investigate the significance of autophagy in lipid metabolism, we performed an extensive lipidomic characterization of Arabidopsis (Arabidopsis thaliana) autophagy mutants (atg) submitted to dark-induced senescence conditions. Our results revealed an altered lipid profile in atg mutants, suggesting that autophagy affects the homeostasis of multiple lipid components under dark-induced senescence. The acute degradation of chloroplast lipids coupled with the differential accumulation of triacylglycerols (TAGs) and plastoglobuli indicates an alternative metabolic reprogramming towards lipid storage in atg mutants. The imbalance of lipid metabolism compromises the production of cytosolic lipid droplets and the regulation of peroxisomal lipid oxidation pathways in atg mutants. One-sentence summaryAutophagy is required for the mobilization of membrane lipid components and lipid droplet dynamics during extended darkness in Arabidopsis.

plant biology↗

bioRxiv2019

Elevated CO2 induces age-dependent restoration of growth and metabolism in gibberellin-deficient plants

Main conclusion The effect of elevated [CO2] on the growth of tomato plants with reduced GA content is influenced by developmental stage. The increase of carbon dioxide (CO2) in the atmosphere during the last decades has aroused interest in the function of this gas in the growth and development of plants. Despite the known association between elevated CO2 concentration ([CO2]) and plant growth, its effects in association with gibberellin (GA), plant hormone that regulates de major aspects of plant growth, are still poorly understood. Therefore, we evaluated the effect of elevated [CO2] on growth and primary metabolism in tomato plants with drastic reduction in GA content (gib-1) at two different growth stages (21 and 35 days after germination, dag). Disruption on growth, photosynthetic parameters and primary metabolism were restored when gib-1 plants were transferred to elevated [CO2] at 21 dag. Elevated [CO2] also stimulated growth and photosynthetic parameters in Wild type (WT) plants at 21 dag, however, minor changes were observed in the level of primary metabolites. At 35 dag, elevated [CO2] did not stimulate growth in WT plants and gib-1 mutants showed their characteristic stunted growth phenotype.

plant biology↗

bioRxiv2018

SELF-PRUNING affects auxin responses synergistically with the cyclophilin A DIAGEOTROPICA in tomato

SummaryThe antiflorigenic signal SELF-PRUNING, which controls growth habit, exerts its effects through auxin transport, signaling and metabolism in tomato.\n\nAbstractThe SELF PRUNING (SP) gene is a key regulator of growth habit in tomato (Solanum lycopersicum). It is an ortholog of TERMINAL FLOWER 1, a phosphatidyl-ethanolamine binding protein with anti-florigenic activity in Arabidopsis thaliana. A spontaneous loss-of-function sp mutation has been bred into a large number of industrial tomato cultivars, as it produces a suite of pleiotropic effects that are favorable for mechanical harvesting, including determinate growth habit, short plant stature and simultaneous fruit ripening. However, the physiological basis for these phenotypic differences has not been thoroughly explained. Here, we show that the sp mutation alters polar auxin transport as well as auxin responses such gravitropic curvature and elongation of excised hypocotyl segments. We further demonstrate that free auxin levels and auxin-regulated gene expression patterns are altered in sp, with epistatic effects of diageotropica, a mutation in a cyclophilin A protein-encoding gene. Our results indicate that SP impacts growth habit in tomato, at least in part, via changes in auxin transport and responsiveness. These findings hint at novel targets that could be manipulated in the control of growth habit and productivity.

plant biology↗

bioRxiv2017

Bundle sheath extensions in tomato affect leaf phenotypic plasticity in response to irradiance

Coordination between structural and physiological traits is key to plants responses to environmental fluctuations. In heterobaric leaves, bundle sheath extensions (BSEs) increase photosynthetic performance (light-saturated rates of photosynthesis, Amax) and water transport capacity (leaf hydraulic conductance, Kleaf). However, it is not clear how BSEs affect these and other leaf developmental and physiological parameters in response to environmental conditions. The obscuravenosa (obv) mutation, found in many commercial tomato varieties, leads to absence of BSEs. We examined structural and physiological traits of tomato heterobaric and homobaric (obv) near-isogenic lines (NILs) grown at two different irradiance levels. Kleaf, minor vein density and stomatal pore area index decreased with shading in heterobaric but not in homobaric leaves, which show similarly lower values in both conditions. Homobaric plants, on the other hand, showed increased Amax, leaf intercellular air spaces and mesophyll surface area exposed to intercellular airspace (Smes) in comparison with heterobaric plants when both were grown in the shade. BSEs further affected carbon isotope discrimination, a proxy for long-term water-use efficiency. BSEs confer plasticity in traits related to leaf structure and function in response to irradiance levels and might act as a hub integrating leaf structure, photosynthetic function and water supply and demand.\n\nSummary statementThe presence of bundle sheath extension (BSEs) defines leaves as heterobaric, as opposed to homobaric leaves that lack them. Multiple functions have been proposed for BSEs, but their impact on different environmental conditions is still unclear. Here, we compared a tomato (Solanum lycopersicum) homobaric mutant lacking BSEs with its corresponding heterobaric wild-type, grown under two irradiance conditions. We show that the presence of BSEs differentially alters various physiological and anatomical parameters in response to growth irradiance. We propose that BSEs could act as hubs coordinating leaf plasticity in response to environmental factors.\n\nArticle typeResearch article

plant biology↗