A tomato B-box protein regulates plant development and fruit quality through the interaction with PIF4, HY5 and RIN transcription factors

During the last decade, the knowledge about BBX proteins has abruptly increased. Genome-wide studies identified BBX gene family in several ornamental, industry and food crops; however, the reports regarding the role of these genes as regulators of agronomically important traits are scarce. Here, by phenotyping a knockout mutant, we performed a comprehensive functional characterization of the tomato locus Solyc12g089240, hereafter called SlBBX20. The data revealed the encoded protein as a positive regulator of light signaling affecting several physiological processes during plant lifespan. By the inhibition of PHYTOCHROME INTERACTING FACTOR 4 (SlPIF4)-auxin crosstalk, SlBBX20 regulates photomorphogenesis. Later, it controls the balance between cell division and expansion to guarantee the correct vegetative and reproductive development. In fruits, SlBBX20 is transcriptionally induced by the master transcription factor RIPENING INHIBITOR (SlRIN) and, together with ELONGATED HYPOCOTYL 5 (SlHY5), upregulates flavonoids biosynthetic genes. Finally, SlBBX20 promotes the accumulation of steroidal glycoalkaloids and attenuates Botrytis cinerea infection. This work clearly demonstrates that BBX proteins are multilayer regulators of plant physiology, not only because they affect multiple processes along plant development but also regulate other genes at the transcriptional and post-translational levels.

Carotenoids and Tocopherol Profiling in Fleshy Fruits

Carotenoids and tocopherols are among the most powerful lipophilic antioxidants accumulated in fruit and vegetable crops. This chapter describes a method for the separation and quantification of carotenoids/chlorophylls and tocopherols based on microextraction followed by reverse- and normal-phase HPLC, respectively. Using this method, high-throughput, accurate analysis of these compounds can be performed in leaf and fruit samples.

Loss of S-nitrosoglutathione reductase disturbs phytohormone homeostasis and regulates shoot side branching and fruit growth in tomato

S-Nitrosoglutathione plays a central role in nitric oxide (NO) homeostasis, and S-nitrosoglutathione reductase (GSNOR) regulates the cellular levels of S-nitrosoglutathione across kingdoms. Here, we investigated the role of endogenous NO in shaping shoot architecture and controlling fruit set and growth in tomato (Solanum lycopersicum). SlGSNOR silencing promoted shoot side branching and led to reduced fruit size, negatively impacting fruit yield. Greatly intensified in slgsnor knockout plants, these phenotypical changes were virtually unaffected by SlGSNOR overexpression. Silencing or knocking out of SlGSNOR intensified protein tyrosine nitration and S-nitrosation and led to aberrant auxin production and signaling in leaf primordia and fruit-setting ovaries, besides restricting the shoot basipetal polar auxin transport stream. SlGSNOR deficiency triggered extensive transcriptional reprogramming at early fruit development, reducing pericarp cell proliferation due to restrictions on auxin, gibberellin, and cytokinin production and signaling. Abnormal chloroplast development and carbon metabolism were also detected in early-developing NO-overaccumulating fruits, possibly limiting energy supply and building blocks for fruit growth. These findings provide new insights into the mechanisms by which endogenous NO fine-tunes the delicate hormonal network controlling shoot architecture, fruit set, and post-anthesis fruit development, emphasizing the relevance of NO-auxin interaction for plant development and productivity.

Tomato miR156-targeted SlSBP15 represses shoot branching by modulating hormone dynamics and interacting with GOBLET and BRANCHED1b

The miRNA156 (miR156)/SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL/SBP) regulatory hub is highly conserved among phylogenetically distinct species, but how it interconnects multiple pathways to converge to common integrators controlling shoot architecture is still unclear. Here, we demonstrated that the miR156/SlSBP15 node modulates tomato shoot branching by connecting multiple phytohormones with classical genetic pathways regulating both axillary bud development and outgrowth. miR156-overexpressing plants (156-OE) displayed high shoot branching, whereas plants overexpressing a miR156-resistant SlSBP15 allele (rSBP15) showed arrested shoot branching. Importantly, the rSBP15 allele was able to partially restore the wild-type shoot branching phenotype in the 156-OE background. rSBP15 plants have tiny axillary buds, and their activation is dependent on shoot apex-derived auxin transport inhibition. Hormonal measurements revealed that indole-3-acetic acid (IAA) and abscisic acid (ABA) concentrations were lower in 156-OE and higher in rSBP15 axillary buds, respectively. Genetic and molecular data indicated that SlSBP15 regulates axillary bud development and outgrowth by inhibiting auxin transport and GOBLET (GOB) activity, and by interacting with tomato BRANCHED1b (SlBRC1b) to control ABA levels within axillary buds. Collectively, our data provide a new mechanism by which the miR156/SPL/SBP hub regulates shoot branching, and suggest that modulating SlSBP15 activity might have potential applications in shaping tomato shoot architecture.

Phytol recycling: essential, yet not limiting for tomato fruit tocopherol accumulation under normal growing conditions

Tocopherols are potent membrane-bound antioxidant molecules that are paramount for plant physiology and also important for human health. In the past years, chlorophyll catabolism was identified as the primary source of phytyl diphosphate for tocopherol synthesis by the action of two enzymes, PHYTOL KINASE (VTE5) and PHYTHYL PHOSPHATE KINASE (VTE6) that are able to recycle the chlorophyll-derived phytol. While VTE5 and VTE6 were proven essential for tocopherol metabolism in tomato fruits, it remains unknown whether they are rate-limiting steps in this pathway. To address this question, transgenic tomato plants expressing AtVTE5 and AtVTE6 in a fruit-specific manner were generated. Although ripe transgenic fruits exhibited higher amounts of tocopherol, phytol recycling revealed a more intimate association with chlorophyll than with tocopherol content. Interestingly, protein-protein interactions assays showed that VTE5 and VTE6 are complexed, channeling free phytol and phytyl-P, thus mitigating their cytotoxic nature. Moreover, the analysis of tocopherol accumulation dynamics in roots, a chlorophyll-devoid organ, revealed VTE5-dependent tocopherol accumulation, hinting at the occurrence of shoot-to-root phytol trafficking. Collectively, these results demonstrate that phytol recycling is essential for tocopherol biosynthesis, even in chlorophyll-devoid organs, yet it is not the rate-limiting step for this pathway under normal growth conditions.

CRYPTOCHROME 1a-mediated blue light perception regulates tomato seed germination via changes in hormonal balance and endosperm-degrading hydrolase dynamics

Blue light exposure delays tomato seed germination by decreasing endosperm-degrading hydrolase activities, a process regulated by CRY1a-dependent signaling and the hormonal balance between ABA and GA. The germination of tomato seeds (Solanum lycopersicum L.) is tightly controlled by an internal hormonal balance, which is also influenced by environmental factors such as light. In this study, we investigated the blue light (BL)-mediated impacts on physiological, biochemical, and molecular processes during the germination of the blue light photoreceptor CRYPTOCHROME 1a loss-of-function mutant (cry1a) and of the hormonal tomato mutants notabilis (not, deficient in ABA) and procera (pro, displaying a GA-constitutive response). Seeds were germinated in a controlled chamber in the dark and under different intensities of continuous BL (ranging from 1 to 25 µmol m^-2 s^-1). In general, exposure to BL delayed tomato seed germination in a fluency rate-dependent way due to negative impacts on the activities of endosperm-degrading hydrolases, such as endo-β-mannanase, β-mannosidase, and α-galactosidase. However, not and pro mutants presented higher germination speed index (GSI) compared to WT despite the BL influence, associated with higher hydrolase activities, especially evident in pro, indicating that the ABA/GA hormonal balance is important to diminish BL inhibition over tomato germination. The cry1a germination percentage was higher than in WT in the dark but its GSI was lower under BL exposure, suggesting that functional CRY1a is required for BL-dependent germination. BL inhibits the expression of GA-biosynthetic genes, and induces GA-deactivating and ABA-biosynthetic genes. The magnitude of the BL influence over the hormone-related transcriptional profile is also dependent upon CRY1a, highlighting the complex interplay between light and hormonal pathways. These results contribute to a better understanding of BL-induced events behind the photoregulation of tomato seed germination.

Fruit Physiology through Signaling Processes: Latest Advances and Future Challenges

Fruits are unique to flowering plants and confer a selective advantage to these species by facilitating seed maturation and dispersal [...].

SlBBX28 positively regulates plant growth and flower number in an auxin-mediated manner in tomato

SlBBX28 is a positive regulator of auxin metabolism and signaling, affecting plant growth and flower number in tomato B-box domain-containing proteins (BBXs) comprise a family of transcription factors that regulate several processes, such as photomorphogenesis, flowering, and stress responses. For this reason, attention is being directed toward the functional characterization of these proteins, although knowledge in species other than Arabidopsis thaliana remains scarce. Particularly in the tomato, Solanum lycopersicum, only three out of 31 SlBBX proteins have been functionally characterized to date. To deepen the understanding of the role of these proteins in tomato plant development and yield, SlBBX28, a light-responsive gene, was constitutively silenced, resulting in plants with smaller leaves and fewer flowers per inflorescence. Moreover, SlBBX28 knockdown reduced hypocotyl elongation in darkness-grown tomato. Analyses of auxin content and responsiveness revealed that SlBBX28 promotes auxin-mediated responses. Altogether, the data revealed that SlBBX28 promotes auxin production and signaling, ultimately leading to proper hypocotyl elongation, leaf expansion, and inflorescence development, which are crucial traits determining tomato yield.

Auxin-driven ecophysiological diversification of leaves in domesticated tomato

Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalize the parenchyma, whereas homobaric leaves do not. The presence of BSEs affects leaf hydraulics and photosynthetic rate. The tomato (Solanum lycopersicum) obscuravenosa (obv) mutant lacks BSEs. Here, we identify the obv gene and the causative mutation, a nonsynonymous amino acid change that disrupts a C2H2 zinc finger motif in a putative transcription factor. This mutation exists as a polymorphism in the natural range of wild tomatoes but has increased in frequency in domesticated tomatoes, suggesting that the latter diversified into heterobaric and homobaric leaf types. The obv mutant displays reduced vein density, leaf hydraulic conductance and photosynthetic assimilation rate. We show that these and other pleiotropic effects on plant development, including changes in leaf insertion angle, leaf margin serration, minor vein density, and fruit shape, are controlled by OBV via changes in auxin signaling. Loss of function of the transcriptional regulator AUXIN RESPONSE FACTOR 4 (ARF4) also results in defective BSE development, revealing an additional component of a genetic module controlling aspects of leaf development important for ecological adaptation and subject to breeding selection.

A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism in Portulaca oleracea

Portulaca species can switch between C4 and crassulacean acid metabolism (CAM) depending on environmental conditions. However, the regulatory mechanisms behind this rare photosynthetic adaptation remain elusive. Using Portulaca oleracea as a model system, here we investigated the involvement of the circadian clock, plant hormones, and transcription factors in coordinating C4 and CAM gene expression. Free-running experiments in constant conditions suggested that C4 and CAM gene expression are intrinsically connected to the circadian clock. Detailed time-course, drought, and rewatering experiments revealed distinct time frames for CAM induction and reversion (days versus hours, respectively), which were accompanied by changes in abscisic acid (ABA) and cytokinin metabolism and signaling. Exogenous ABA and cytokinins were shown to promote and repress CAM expression in P. oleracea, respectively. Moreover, the drought-induced decline in C4 transcript levels was completely recovered upon cytokinin treatment. The ABA-regulated transcription factor genes HB7, NFYA7, NFYC9, TT8, and ARR12 were identified as likely candidate regulators of CAM induction following this approach, whereas NFYC4 and ARR9 were connected to C4 expression patterns. Therefore, we provide insights into the signaling events controlling C4-CAM transitions in response to water availability and over the day/night cycle, highlighting candidate genes for future functional studies in the context of facultative C4-CAM photosynthesis.

Drought tolerance memory transmission by citrus buds

Plants face recurrent drought events, and previous stresses can influence their responses to subsequent stress episodes. Studies on drought stress memory are recent in citriculture, although they show promise as a tool for crop improvement. Here, we investigated whether stress memory mechanisms can be detected in citrus plants grafted with buds from plants subjected to recurrent water deficit. Three rootstock varieties, namely 'Rangpur Santa Cruz' lime, 'Sunki Maravilha' mandarin and 'Sunki Tropical' mandarin, in combination with 'Valencia' orange, were either maintained under full irrigation or subjected to one, two, or three water deficit cycles. Buds from 'Valencia' orange were grafted onto 'Swingle' citrumelo rootstocks and were evaluated. This combination displayed improved physiological and biochemical performance under water limitation, especially 'Valencia' buds grafted onto 'Sunki Maravilha', with better photosynthetic performance under water deficit. These findings indicate that genotype-dependent epigenetic memory is a key factor in restoring citrus plants' capacity to rely on previous stress experiences to restore better photosynthetic and physiological responses when undergoing new water deficit events. Therefore, epigenetic marks can be stored and transmitted to new citrus plants and are a promising alternative to enable increased water deficit tolerance when plants are then challenged by drought-prone environments.

Proteomic Analysis of S-Nitrosation Sites During Somatic Embryogenesis in Brazilian Pine, Araucaria angustifolia (Bertol.) Kuntze

Cysteine S-nitrosation is a redox-based post-translational modification that mediates nitric oxide (NO) regulation of various aspects of plant growth, development and stress responses. Despite its importance, studies exploring protein signaling pathways that are regulated by S-nitrosation during somatic embryogenesis have not been performed. In the present study, endogenous cysteine S-nitrosation site and S-nitrosated proteins were identified by iodo-TMT labeling during somatic embryogenesis in Brazilian pine, an endangered native conifer of South America. In addition, endogenous -S-nitrosothiol (SNO) levels and S-nitrosoglutathione reductase (GSNOR) activity were determined in cell lines with contrasting embryogenic potential. Overall, we identified an array of proteins associated with a large variety of biological processes and molecular functions with some of them already described as important for somatic embryogenesis (Class IV chitinase, pyruvate dehydrogenase E1 and dehydroascorbate reductase). In total, our S-nitrosoproteome analyses identified 18 endogenously S-nitrosated proteins and 50 in vitro S-nitrosated proteins (after GSNO treatment) during cell culture proliferation and embryo development. Furthermore, SNO levels and GSNOR activity were increased during embryo formation. These findings expand our understanding of the Brazilian pine proteome and shed novel insights into the potential use of pharmacological manipulation of NO levels by using NO inhibitors and donors during somatic embryogenesis.

Increased branching independent of strigolactone in cytokinin oxidase 2-overexpressing tomato is mediated by reduced auxin transport

Tomato production is influenced by shoot branching, which is controlled by different hormones. Here we produced tomato plants overexpressing the cytokinin-deactivating gene CYTOKININ OXYDASE 2 (CKX2). CKX2-overexpressing (CKX2-OE) plants showed an excessive growth of axillary shoots, the opposite phenotype expected for plants with reduced cytokinin content, as evidenced by LC-MS analysis and ARR5-GUS staining. The TCP transcription factor SlBRC1b was downregulated in the axillary buds of CKX2-OE and its excessive branching was dependent on a functional version of the GRAS-family gene LATERAL SUPPRESSOR (LS). Grafting experiments indicated that increased branching in CKX2-OE plants is unlikely to be mediated by root-derived signals. Crossing CKX2-OE plants with transgenic antisense plants for the strigolactone biosynthesis gene CAROTENOID CLEAVAGE DIOXYGENASE (CCD7-AS) produced an additive phenotype, indicating independent effects of cytokinin and strigolactones on increased branching. On the other hand, CKX2-OE plants showed reduced polar auxin transport and their bud outgrowth was reduced when combined with auxin mutants. Accordingly, CKX2-OE basal buds did not respond to auxin applied in the decapitated apex. Our results suggest that tomato shoot branching depends on a fine-tuning of different hormonal balances and that perturbations in the auxin status could compensate for the reduced cytokinin levels in CKX2-OE plants.

Phytochrome-Mediated Light Perception Affects Fruit Development and Ripening Through Epigenetic Mechanisms

Phytochrome (PHY)-mediated light and temperature perception has been increasingly implicated as important regulator of fruit development, ripening, and nutritional quality. Fruit ripening is also critically regulated by chromatin remodeling via DNA demethylation, though the molecular basis connecting epigenetic modifications in fruits and environmental cues remains largely unknown. Here, to unravel whether the PHY-dependent regulation of fruit development involves epigenetic mechanisms, an integrative analysis of the methylome, transcriptome and sRNAome of tomato fruits from phyA single and phyB1B2 double mutants was performed in immature green (IG) and breaker (BK) stages. The transcriptome analysis showed that PHY-mediated light perception regulates more genes in BK than in the early stages of fruit development (IG) and that PHYB1B2 has a more substantial impact than PHYA in the fruit transcriptome, in both analyzed stages. The global profile of methylated cytosines revealed that both PHYA and PHYB1B2 affect the global methylome, but PHYB1B2 has a greater impact on ripening-associated methylation reprogramming across gene-rich genomic regions in tomato fruits. Remarkably, promoters of master ripening-associated transcription factors (TF) (RIN, NOR, CNR, and AP2a) and key carotenoid biosynthetic genes (PSY1, PDS, ZISO, and ZDS) remained highly methylated in phyB1B2 from the IG to BK stage. The positional distribution and enrichment of TF binding sites were analyzed over the promoter region of the phyB1B2 DEGs, exposing an overrepresentation of binding sites for RIN as well as the PHY-downstream effectors PIFs and HY5/HYH. Moreover, phyA and phyB1B2 mutants showed a positive correlation between the methylation level of sRNA cluster-targeted genome regions in gene bodies and mRNA levels. The experimental evidence indicates that PHYB1B2 signal transduction is mediated by a gene expression network involving chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes, and remodeling factors) and transcriptional regulators leading to altered mRNA profile of ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits.

Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao, interferes with cytokinin metabolism during infection of Micro-Tom tomato and promotes symptom development

Moniliophthora perniciosa causes witches' broom disease of cacao and inflicts symptoms suggestive of hormonal imbalance. We investigated whether infection of the tomato (Solanum lycopersicum) model system Micro-Tom (MT) by the Solanaceae (S)-biotype of Moniliophthora perniciosa, which causes stem swelling and hypertrophic growth of axillary shoots, results from changes in host cytokinin metabolism. Inoculation of an MT-transgenic line that overexpresses the Arabidopsis CYTOKININ OXIDASE-2 gene (35S::AtCKX2) resulted in a reduction in disease incidence and stem diameter. RNA-sequencing analysis of infected MT and 35S::AtCKX2 revealed the activation of cytokinin-responsive marker genes when symptoms were conspicuous. The expression of an Moniliophthora perniciosa tRNA-ISOPENTENYL-TRANSFERASE suggests the production of isopentenyladenine (iP), detected in mycelia grown in vitro. Inoculated MT stems showed higher levels of dihydrozeatin and trans-zeatin but not iP. The application of benzyladenine induced symptoms similar to infection, whereas applying the cytokinin receptor inhibitors LGR-991 and PI55 decreased symptoms. Moniliophthora perniciosa produces iP that might contribute to cytokinin synthesis by the host, which results in vascular and cortex enlargement, axillary shoot outgrowth, reduction in root biomass and an increase in fruit locule number. This strategy may be associated with the manipulation of sink establishment to favour infection by the fungus.

Developing Portulaca oleracea as a model system for functional genomics analysis of C4/CAM photosynthesis

Previously regarded as an intriguing photosynthetic curiosity, the occurrence of C4 and Crassulacean acid metabolism (CAM) photosynthesis within a single organism has recently emerged as a source of information for future biotechnological use. Among C4/CAM facultative species, Portulaca oleracea L. has been used as a model for biochemical and gene expression analysis of C4/CAM under field and laboratory conditions. In the present work, we focussed on developing molecular tools to facilitate functional genomics studies in this species, from the optimisation of RNA isolation protocols to a method for stable genetic transformation. Eleven variations of RNA extraction procedures were tested and compared for RNA quantity and quality. Also, 7 sample sets comprising total RNA from hormonal and abiotic stress treatments, distinct plant organs, leaf developmental stages, and subspecies were used to select, among 12 reference genes, the most stable reference genes for RT-qPCR analysis of each experimental condition. Furthermore, different explant sources, Agrobacterium tumefaciens strains, and regeneration and antibiotic selection media were tested in various combinations to optimise a protocol for stable genetic transformation of P. oleracea. Altogether, we provide essential tools for functional gene analysis in the context of C4/CAM photosynthesis, including an efficient RNA isolation method, preferred reference genes for RT-qPCR normalisation for a range of experimental conditions, and a protocol to produce P. oleracea stable transformants using A. tumefaciens.

Multifaceted roles of nitric oxide in tomato fruit ripening: NO-induced metabolic rewiring and consequences for fruit quality traits

Nitric oxide (NO) has been implicated as part of the ripening regulatory network in fleshy fruits. However, very little is known about the simultaneous action of NO on the network of regulatory events and metabolic reactions behind ripening-related changes in fruit color, taste, aroma and nutritional value. Here, we performed an in-depth characterization of the concomitant changes in tomato (Solanum lycopersicum) fruit transcriptome and metabolome associated with the delayed-ripening phenotype caused by NO supplementation at the pre-climacteric stage. Approximately one-third of the fruit transcriptome was altered in response to NO, including a multilevel down-regulation of ripening regulatory genes, which in turn restricted the production and tissue sensitivity to ethylene. NO also repressed hydrogen peroxide-scavenging enzymes, intensifying nitro-oxidative stress and S-nitrosation and nitration events throughout ripening. Carotenoid, tocopherol, flavonoid and ascorbate biosynthesis were differentially affected by NO, resulting in overaccumulation of ascorbate (25%) and flavonoids (60%), and impaired lycopene production. In contrast, the biosynthesis of compounds related to tomato taste (sugars, organic acids, amino acids) and aroma (volatiles) was slightly affected by NO. Our findings indicate that NO triggers extensive transcriptional and metabolic rewiring at the early ripening stage, modifying tomato antioxidant composition with minimal impact on fruit taste and aroma.

The light and dark sides of nitric oxide: multifaceted roles of nitric oxide in plant responses to light

Light drives photosynthesis and informs plants about their surroundings. Regarded as a multifunctional signaling molecule in plants, nitric oxide (NO) has been repeatedly demonstrated to interact with light signaling cascades to control plant growth, development and metabolism. During early plant development, light-triggered NO accumulation counteracts negative regulators of photomorphogenesis and modulates the abundance of, and sensitivity to, plant hormones to promote seed germination and de-etiolation. In photosynthetically active tissues, NO is generated at distinct rates under light or dark conditions and acts at multiple target sites within chloroplasts to regulate photosynthetic reactions. Moreover, changes in NO concentrations in response to light stress promote plant defenses against oxidative stress under high light or ultraviolet-B radiation. Here we review the literature on the interaction of NO with the complicated light and hormonal signaling cascades controlling plant photomorphogenesis and light stress responses, focusing on the recently identified molecular partners and action mechanisms of NO in these events. We also discuss the versatile role of NO in regulating both photosynthesis and light-dependent stomatal movements, two key determinants of plant carbon gain. The regulation of nitrate reductase (NR) by light is highlighted as vital to adjust NO production in plants living under natural light conditions.

Ethylene and Auxin: Hormonal Regulation of Volatile Compound Production During Tomato (Solanum lycopersicum L.) Fruit Ripening

As the auxin-ethylene interaction in climacteric fruit ripening has been highlighted, the hormonal regulation of aroma changes in climacteric fruits requires clarification. The influence of both phytohormones on the volatile organic compound (VOC) metabolism was evaluated during tomato (Solanum lycopersicum L.) fruit ripening. Tomato fruits cv. Micro-Tom and Sweet Grape at the mature green stage were randomly grouped according to treatment with ethylene (ETHY), auxin (IAA), or both (ETHY + IAA). At middle ripening, Micro-Tom ETHY + IAA fruits present VOC profiles similar to those of ETHY fruits, while Sweet Grape presents VOC profiles closer to those of IAA fruits. At full ripeness, Micro-Tom and Sweet Grape ETHY + IAA fruits show profiles closer to those of IAA fruits, suggesting that the auxin overlaps the ethylene effects. Aroma compounds positively correlated with consumer preferences (2-isobutylthiazole, 6-methyl-5-hepten-2-one, and others) are identified in both cultivars and have their contents affected by both hormone treatments. The transcription of genes related to the biosynthesis of important tomato VOCs that have fatty-acid and carotenoid precursors evidences their regulation by both plant hormones. Additionally, the results indicate that the observed effects on the VOC metabolism are not restricted to the Micro-Tom cultivar, as these are also observed in the Sweet Grape cultivar. In conclusion, ethylene and auxin directly regulate the metabolic pathways related to VOC formation, impacting tomato aroma formation during ripening since Micro-Tom fruits apparently at the same maturation stage have different aromas.

Light and ripening-regulated BBX protein-encoding genes in Solanum lycopersicum

Light controls several aspects of plant development through a complex signalling cascade. Several B-box domain containing proteins (BBX) were identified as regulators of Arabidopsis thaliana seedling photomorphogenesis. However, the knowledge about the role of this protein family in other physiological processes and species remains scarce. To fill this gap, here BBX protein encoding genes in tomato genome were characterised. The robust phylogeny obtained revealed how the domain diversity in this protein family evolved in Viridiplantae and allowed the precise identification of 31 tomato SlBBX proteins. The mRNA profiling in different organs revealed that SlBBX genes are regulated by light and their transcripts accumulation is directly affected by the chloroplast maturation status in both vegetative and fruit tissues. As tomato fruits develops, three SlBBXs were found to be upregulated in the early stages, controlled by the proper chloroplast differentiation and by the PHYTOCHROME (PHY)-dependent light perception. Upon ripening, other three SlBBXs were transcriptionally induced by RIPENING INHIBITOR master transcriptional factor, as well as by PHY-mediated signalling and proper plastid biogenesis. Altogether, the results obtained revealed a conserved role of SlBBX gene family in the light signalling cascade and identified putative members affecting tomato fruit development and ripening.

Beyond the limits of photoperception: constitutively active PHYTOCHROME B2 overexpression as a means of improving fruit nutritional quality in tomato

Photoreceptor engineering has recently emerged as a means for improving agronomically beneficial traits in crop species. Despite the central role played by the red/far-red photoreceptor phytochromes (PHYs) in controlling fruit physiology, the applicability of PHY engineering for increasing fleshy fruit nutritional content remains poorly exploited. In this study, we demonstrated that the fruit-specific overexpression of a constitutively active GAF domain Tyr252 -to-His PHYB2 mutant version (PHYB2Y252H ) significantly enhances the accumulation of multiple health-promoting antioxidants in tomato fruits, without negative collateral consequences on vegetative development. Compared with the native PHYB2 overexpression, PHYB2Y252H -overexpressing lines exhibited more extensive increments in transcript abundance of genes associated with fruit plastid development, chlorophyll biosynthesis and metabolic pathways responsible for the accumulation of antioxidant compounds. Accordingly, PHYB2Y252H -overexpressing fruits developed more chloroplasts containing voluminous grana at the green stage and overaccumulated carotenoids, tocopherols, flavonoids and ascorbate in ripe fruits compared with both wild-type and PHYB2-overexpressing lines. The impacts of PHYB2 or PHYB2Y252H overexpression on fruit primary metabolism were limited to a slight promotion in lipid biosynthesis and reduction in sugar accumulation. Altogether, these findings indicate that mutation-based adjustments in PHY properties represent a valuable photobiotechnological tool for tomato biofortification, highlighting the potential of photoreceptor engineering for improving quality traits in fleshy fruits.

Exploring C4-CAM plasticity within the Portulaca oleracea complex

Portulaca oleracea is a C₄ herb capable of performing CAM under drought stress. It is distributed worldwide and is either considered a polymorphic species or a complex of subspecies, due to its numerous morphological variations. We evaluated CAM plasticity within P. oleracea genotypes since the complexity surrounding this species may be reflected in intraspecific variations in photosynthetic behavior. Eleven subspecies of P. oleracea from distant geographical locations and one cultivar were morphologically and physiologically characterized. C₄ and CAM photosynthesis were monitored in plants exposed to well-watered, droughted and rewatered treatments, and data obtained were compared among individual genotypes. All subspecies expressed CAM in a fully-reversible manner. Transcript abundance of C₄–CAM signature genes was shown to be a useful indicator of the C₄–CAM–C₄ switches in all genotypes. C₄-related genes were down-regulated and subsequently fully expressed upon drought and rewatering, respectively. CAM-marker genes followed the opposite pattern. A gradient of morphological traits and drought-induced nighttime malate accumulation was observed across genotypes. Therefore, different combinations of CAM expression levels, plant sizes and shapes are available within the P. oleracea complex, which can be a valuable tool in the context of C₄/CAM photosynthesis research.

Phytochrome-Dependent Temperature Perception Modulates Isoprenoid Metabolism

Changes in environmental temperature influence many aspects of plant metabolism; however, the underlying regulatory mechanisms remain poorly understood. In addition to their role in light perception, phytochromes (PHYs) have been recently recognized as temperature sensors affecting plant growth. In particular, in Arabidopsis (Arabidopsis thaliana), high temperature reversibly inactivates PHYB, reducing photomorphogenesis-dependent responses. Here, we show the role of phytochrome-dependent temperature perception in modulating the accumulation of isoprenoid-derived compounds in tomato (Solanum lycopersicum) leaves and fruits. The growth of tomato plants under contrasting temperature regimes revealed that high temperatures resulted in coordinated up-regulation of chlorophyll catabolic genes, impairment of chloroplast biogenesis, and reduction of carotenoid synthesis in leaves in a PHYB1B2-dependent manner. Furthermore, by assessing a triple phyAB1B2 mutant and fruit-specific PHYA- or PHYB2-silenced plants, we demonstrated that biosynthesis of the major tomato fruit carotenoid, lycopene, is sensitive to fruit-localized PHY-dependent temperature perception. The collected data provide compelling evidence concerning the impact of PHY-mediated temperature perception on plastid metabolism in both leaves and fruit, specifically on the accumulation of isoprenoid-derived compounds.

C4 and crassulacean acid metabolism within a single leaf: deciphering key components behind a rare photosynthetic adaptation

Although biochemically related, C₄ and crassulacean acid metabolism (CAM) systems are expected to be incompatible. However, Portulaca species, including P. oleracea, operate C₄ and CAM within a single leaf, and the mechanisms behind this unique photosynthetic arrangement remain largely unknown. Here, we employed RNA-seq to identify candidate genes involved exclusively or shared by C₄ or CAM, and provided an in-depth characterization of their transcript abundance patterns during the drought-induced photosynthetic transitions in P. oleracea. Data revealed fewer candidate CAM-specific genes than those recruited to function in C₄ . The putative CAM-specific genes were predominantly involved in night-time primary carboxylation reactions and malate movement across the tonoplast. Analysis of gene transcript-abundance regulation and photosynthetic physiology indicated that C₄ and CAM coexist within a single P. oleracea leaf under mild drought conditions. Developmental and environmental cues were shown to regulate CAM expression in stems, whereas the shift from C₄ to C₄ -CAM hybrid photosynthesis in leaves was strictly under environmental control. Moreover, efficient starch turnover was identified as part of the metabolic adjustments required for CAM operation in both organs. These findings provide insights into C₄ /CAM connectivity and compatibility, contributing to a deeper understanding of alternative ways to engineer CAM into C₄ crop species.

Downregulation of PHYTOCHROME-INTERACTING FACTOR 4 Influences Plant Development and Fruit Production

Plant development is highly dependent on the ability to perceive and cope with environmental changes. In this context, PIF proteins are key players in the cellular hub controlling responses to fluctuating light and temperature conditions. Reports in various plant species show that manipulation of the PIF4 level affects important agronomical traits. In tomato (Solanum lycopersicum), SlPIF1a and SlPIF3 regulate fruit nutraceutical composition. However, the wider role of this protein family, and the potential of their manipulation for the improvement of other traits, has not been explored. Here we report the effects of constitutive silencing of tomato SlPIF4 on whole-plant physiology and development. Ripening anticipation and higher carotenoid levels observed in SlPIF4-silenced fruits revealed a redundant role of SlPIF4 in the accumulation of nutraceutical compounds. Furthermore, silencing triggered a significant reduction in plant size, flowering, fruit yield, and fruit size. This phenotype was most likely caused by reduced auxin levels and altered carbon partitioning. Impaired thermomorphogenesis and delayed leaf senescence were also observed in silenced plants, highlighting the functional conservation of PIF4 homologs in angiosperms. Overall, this work improves our understanding of the role of PIF proteins-and light signaling-in metabolic and developmental processes that affect yield and composition of fleshy fruits.

Nitric oxide in the physiology and quality of fleshy fruits

Fruits are unique to flowering plants and confer a selective advantage as they facilitate seed maturation and dispersal. In fleshy fruits, development and ripening are associated with numerous structural, biochemical, and physiological changes, including modifications in the general appearance, texture, flavor, and aroma, which ultimately convert the immature fruit into a considerably more attractive and palatable structure for seed dispersal by animals. Treatment with exogenous nitric oxide (NO) delays fruit ripening, prevents chilling damage, promotes disease resistance, and enhances the nutritional value. The ripening process is influenced by NO, which operates antagonistically to ethylene, but it also interacts with other regulatory molecules such as abscisic acid, auxin, jasmonic acid, salicylic acid, melatonin, and hydrogen sulfide. NO content progressively declines during fruit ripening, with concomitant increases in protein nitration and nitrosation, two post-translational modifications that are promoted by reactive nitrogen species. Dissecting the intimate interactions of NO with other ripening-associated factors, including reactive oxygen species, antioxidants, and the aforementioned phytohormones, remains a challenging subject of research. In this context, integrative 'omics' and gene-editing approaches may provide additional knowledge of the impact of NO in the regulatory processes involved in controlling physiology and quality traits in both climacteric and non-climacteric fruits.

Gasotransmitters in Action: Nitric Oxide-Ethylene Crosstalk during Plant Growth and Abiotic Stress Responses

Since their first description as atmospheric gases, it turned out that both nitric oxide (NO) and ethylene (ET) are multifunctional plant signals. ET and polyamines (PAs) use the same precursor for their synthesis, and NO can be produced from PA oxidation. Therefore, an indirect metabolic link between NO and ET synthesis can be considered. NO signal is perceived primarily through S-nitrosation without the involvement of a specific receptor, while ET signal is sensed by a well-characterized receptor complex. Both NO and ET are synthetized by plants at various developmental stages (e.g., seeds, fruits) and as a response to numerous environmental factors (e.g., heat, heavy metals) and they mutually regulate each other's levels. Most of the growth and developmental processes (e.g., fruit ripening, de-etiolation) are regulated by NO-ET antagonism, while in abiotic stress responses, both antagonistic (e.g., dark-induced stomatal opening, cadmium-induced cell death) and synergistic (e.g., UV-B-induced stomatal closure, iron deficiency-induced expression of iron acquisition genes) NO-ET interplays have been revealed. Despite the numerous pieces of experimental evidence revealing NO-ET relationships in plants, the picture is far from complete. Understanding the mechanisms of NO-ET interactions may contribute to the increment of yield and intensification of stress tolerance of crop plants in changing environments.

PHYTOCHROME-INTERACTING FACTOR 3 mediates light-dependent induction of tocopherol biosynthesis during tomato fruit ripening

Tocopherols are important antioxidants exclusively produced in plastids that protect the photosynthetic apparatus from oxidative stress. These compounds with vitamin E activity are also essential dietary nutrients for humans. Although the tocopherol biosynthetic pathway has been elucidated, the mechanisms that regulate tocopherol production and accumulation remain elusive. Here, we investigated the regulatory mechanism underlying tocopherol biosynthesis during ripening in tomato fruits, which are an important source of vitamin E. Our results show that ripening under light conditions increases tocopherol fruit content in a phytochrome-dependent manner by the transcriptional regulation of biosynthetic genes. Moreover, we show that light-controlled expression of the GERANYLGERANYL DIPHOSPHATE REDUCTASE (SlGGDR) gene, responsible for the synthesis of the central tocopherol precursor phytyl diphosphate, is mediated by PHYTOCHROME-INTERACTING FACTOR 3 (SlPIF3). In the absence of light, SlPIF3 physically interacts with the promoter of SlGGDR, down-regulating its expression. By contrast, light activation of phytochromes prevents the interaction between SlPIF3 and the SlGGDR promoter, leading to transcriptional derepression and higher availability of the PDP precursor for tocopherol biosynthesis. The unraveled mechanism provides a new strategy to manipulate fruit metabolism towards improving tomato nutritional quality.

Solanum lycopersicum GOLDEN 2-LIKE 2 transcription factor affects fruit quality in a light- and auxin-dependent manner

Plastids are organelles responsible for essential aspects of plant development, including carbon fixation and synthesis of several secondary metabolites. Chloroplast differentiation and activity are highly regulated by light, and several proteins involved in these processes have been characterised. Such is the case of the GOLDEN 2-LIKE (GLK) transcription factors, which induces the expression of genes related to chloroplast differentiation and photosynthesis. The tomato (Solanum lycopersicum) genome harbours two copies of this gene, SlGLK1 and SlGLK2, each with distinct expression patterns. While the former predominates in leaves, the latter is mainly expressed in fruits, precisely at the pedicel region. During tomato domestication, the selection of fruits with uniform ripening fixed the mutation Slglk2, nowadays present in most cultivated varieties, what penalised fruit metabolic composition. In this study, we investigated how SlGLK2 is regulated by light, auxin and cytokinin and determined the effect of SlGLK2 on tocopherol (vitamin E) and sugar metabolism, which are components of the fruit nutritional and industrial quality. To achieve this, transcriptional profiling and biochemical analysis were performed throughout fruit development and ripening from SlGLK2, Slglk2, SlGLK2-overexpressing genotypes, as well as from phytochrome and hormonal deficient mutants. The results revealed that SlGLK2 expression is regulated by phytochrome-mediated light perception, yet this gene can induce chloroplast differentiation even in a phytochrome-independent manner. Moreover, auxin was found to be a negative regulator of SlGLK2 expression, while SlGLK2 enhances cytokinin responsiveness. Additionally, SlGLK2 enhanced chlorophyll content in immature green fruits, leading to an increment in tocopherol level in ripe fruits. Finally, SlGLK2 overexpression resulted in higher total soluble solid content, possibly by the regulation of sugar metabolism enzyme-encoding genes. The results obtained here shed light on the regulatory network that interconnects SlGLK2, phytohormones and light signal, promoting the plastidial activity and consequently, influencing the quality of tomato fruit.

Recurrent water deficit causes alterations in the profile of redox proteins in citrus plants

Plant acclimation to recurrent stress involves profound alterations in multiple genetic, metabolic and physiological processes. Stressful conditions usually implicate imbalance in reactive oxygen species (ROS) production and removal rates, which may lead to oxidative stress. However, the primary cellular targets of oxidative stress and their relevance in plant acclimation to abiotic stresses remains poorly characterized. By comparing redox proteomic and sugar profiles in citrus Valencia (VO) scions grafted onto two rootstocks with different soil water extraction capacities - Rangpur Lime (RL) and Sunki Maravilha (SM) - here we demonstrate that both ROS-mediated post-translational protein modification and changes in sugar composition are associated with acclimation to recurrent drought in citrus. The redox proteomic analysis of the distinct scion/rootstock combinations exposed to one (WD1), two (WD2) or three (WD3) water deficit episodes revealed a total of 32 and 55 redox protein spots present in VO/RL and VO/SM plants, respectively. Mass spectrometry analysis of these protein spots revealed essential targets of ROS-mediated posttranslational protein modification in citrus plants challenged by recurrent drought. The oxidation of cysteine thiol groups into glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was shown to increase in WD3 samples of the VO/RL combination, whereas the opposite was observed for the VO/SM combination. Similarly, recurrent drought promoted the oxidation of catalase thiol groups in VO/SM, but not in VO/RL. Carbohydrate profiling revealed that glucose, fructose and galactose may also contribute to the phenotypic differences observed between the citrus genotypes exposed to drought. These findings reveal for the first time that recurrent drought differentially affects the profile of redox proteomics of citrus, suggesting that this alteration may be part of the stress memory in perennial plants.

De novo domestication of wild tomato using genome editing

Breeding of crops over millennia for yield and productivity has led to reduced genetic diversity. As a result, beneficial traits of wild species, such as disease resistance and stress tolerance, have been lost. We devised a CRISPR-Cas9 genome engineering strategy to combine agronomically desirable traits with useful traits present in wild lines. We report that editing of six loci that are important for yield and productivity in present-day tomato crop lines enabled de novo domestication of wild Solanum pimpinellifolium. Engineered S. pimpinellifolium morphology was altered, together with the size, number and nutritional value of the fruits. Compared with the wild parent, our engineered lines have a threefold increase in fruit size and a tenfold increase in fruit number. Notably, fruit lycopene accumulation is improved by 500% compared with the widely cultivated S. lycopersicum. Our results pave the way for molecular breeding programs to exploit the genetic diversity present in wild plants.

Fruit-localized phytochromes regulate plastid biogenesis, starch synthesis, and carotenoid metabolism in tomato

Light signaling has long been reported to influence fruit biology, although the regulatory impact of fruit-localized photoreceptors on fruit development and metabolism remains unclear. Studies performed in phytochrome (PHY)-deficient tomato (Solanum lycopersicum) mutants suggest that SlPHYA, SlPHYB2, and to a lesser extent SlPHYB1 influence fruit development and ripening. By employing fruit-specific RNAi-mediated silencing of SlPHY genes, we demonstrated that fruit-localized SlPHYA and SlPHYB2 play contrasting roles in regulating plastid biogenesis and maturation in tomato. Our data revealed that fruit-localized SlPHYA, rather than SlPHYB1 or SlPHYB2, positively influences tomato plastid differentiation and division machinery via changes in both light and cytokinin signaling-related gene expression. Fruit-localized SlPHYA and SlPHYB2 were also shown to modulate sugar metabolism in early developing fruits via overlapping, yet distinct, mechanisms involving the co-ordinated transcriptional regulation of genes related to sink strength and starch biosynthesis. Fruit-specific SlPHY silencing also drastically altered the transcriptional profile of genes encoding light-repressor proteins and carotenoid-biosynthesis regulators, leading to reduced carotenoid biosynthesis during fruit ripening. Together, our data reveal the existence of an intricate PHY-hormonal interplay during fruit development and ripening, and provide conclusive evidence on the regulation of tomato quality by fruit-localized phytochromes.

Nitro-oxidative metabolism during fruit ripening

Pepper (Capsicum annuum L.) and tomato (Solanum lycopersicum L.), which belong to the Solanaceae family, are among the most cultivated and consumed fleshy fruits worldwide and constitute excellent sources of many essential nutrients, such as vitamins A, C, and E, calcium, and carotenoids. While fruit ripening is a highly regulated and complex process, tomato and pepper have been classified as climacteric and non-climacteric fruits, respectively. These fruits differ greatly in shape, color composition, flavor, and several other features which undergo drastic changes during the ripening process. Such ripening-related metabolic and developmental changes require extensive alterations in many cellular and biochemical processes, which ultimately leads to fully ripe fruits with nutritional and organoleptic features that are attractive to both natural dispersers and human consumers. Recent data show that reactive oxygen and nitrogen species (ROS/RNS) are involved in fruit ripening, during which molecules, such as hydrogen peroxide (H2O2), NADPH, nitric oxide (NO), peroxynitrite (ONOO-), and S-nitrosothiols (SNOs), interact to regulate protein functions through post-translational modifications. In light of these recent discoveries, this review provides an update on the nitro-oxidative metabolism during the ripening of two of the most economically important fruits, discusses the signaling roles played by ROS/RNS in controlling this complex physiological process, and highlights the potential biotechnological applications of these substances to promote further improvements in fruit ripening regulation and nutritional quality. In addition, we suggest that the term 'nitro-oxidative eustress' with regard to fruit ripening would be more appropriate than nitro-oxidative stress, which ultimately favors the consolidation of the plant species.

Comparative genomics of a drug-resistant Pseudomonas aeruginosa panel and the challenges of antimicrobial resistance prediction from genomes

Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa. This study focuses on a commercially available panel of seven MDR P. aeruginosa strains. The main goals were to sequence and compare these strains' genomes, attempt to predict AMR from whole genomes using two different methods and determine whether this panel could be an informative complement to the international P. aeruginosa reference panel. As expected, the results highlight the complexity of associating genotype and AMR phenotype in P. aeruginosa, mainly due to the intricate regulation of resistance mechanisms. Our results also urge caution in the interpretation of predicted resistomes regarding the occurrence of gene identity discrepancies between strains. We envision that, in addition to accounting for the genomic diversity of P. aeruginosa, future development of predictive tools will need to incorporate a transcriptomic, proteomic and/or metabolomic component.

SELF-PRUNING Acts Synergistically with DIAGEOTROPICA to Guide Auxin Responses and Proper Growth Form

The SELF PRUNING (SP) gene is a key regulator of growth habit in tomato (Solanum lycopersicum). It is an ortholog of TERMINAL FLOWER1, a phosphatidylethanolamine-binding protein with antiflorigenic activity in Arabidopsis (Arabidopsis thaliana). A spontaneous loss-of-function mutation (sp) has been bred into several 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 as gravitropic curvature and elongation of excised hypocotyl segments. We also demonstrate that free auxin levels and auxin-regulated gene expression patterns are altered in sp mutants. Furthermore, diageotropica, a mutation in a gene encoding a cyclophilin A protein, appears to confer epistatic effects with sp Our results indicate that SP affects the tomato growth habit at least in part by influencing auxin transport and responsiveness. These findings suggest potential novel targets that could be manipulated for controlling plant growth habit and improving productivity.

Volatile organic compounds and nitric oxide as responses of a Brazilian tropical species to ozone: the emission profile of young and mature leaves

The emission profile of volatile organic compounds (VOCs) and nitric oxide (NO) in young and mature leaves of Croton floribundus was assessed in plants exposed to filtered air (FA) and ozone-enriched filtered air (FA+O₃). After the period of exposure, leaves were enclosed in polyethylene terephthalate bags and VOCs were collected in young and mature leaves. Both young and mature leaves constitutively emitted the same VOC, but the concentrations were higher in young leaves. O₃ exposure induced the emission of sesquiterpenes (mainly β-caryophyllene) known as antioxidant compounds that may scavenge O₃. Young leaves were the highest emitters of sesquiterpenes. O₃ induced a rapid accumulation of NO in different tissues and leaf developmental stages; this accumulation was marked in palisade and spongy parenchyma cells in young and mature leaves, respectively. O₃ altered the levels of the signaling compound methyl salicylate (MeSA). Moreover, our data showed that NO together with VOC emissions, such as geranyl acetate, α-cadiene, trans-farnesol, cis-β-farnesene, and MeSA, participate of plant defense mechanisms against the oxidative damage caused by O₃.

Light, Ethylene and Auxin Signaling Interaction Regulates Carotenoid Biosynthesis During Tomato Fruit Ripening

Light signaling and plant hormones, particularly ethylene and auxins, have been identified as important regulators of carotenoid biosynthesis during tomato fruit ripening. However, whether and how the light and hormonal signaling cascades crosstalk to control this metabolic route remain poorly elucidated. Here, the potential involvement of ethylene and auxins in the light-mediated regulation of tomato fruit carotenogenesis was investigated by comparing the impacts of light treatments and the light-hyperresponsive high pigment-2 (hp2) mutation on both carotenoid synthesis and hormonal signaling. Under either light or dark conditions, the overaccumulation of carotenoids in hp2 ripening fruits was associated with disturbed ethylene production, increased expression of genes encoding master regulators of ripening and higher ethylene sensitivity and signaling output. The increased ethylene sensitivity observed in hp2 fruits was associated with the differential expression of genes encoding ethylene receptors and downstream signaling transduction elements, including the downregulation of the transcription factor ETHYLENE RESPONSE FACTOR.E4, a repressor of carotenoid synthesis. Accordingly, treatments with exogenous ethylene promoted carotenoid biosynthetic genes more intensively in hp2 than in wild-type fruits. Moreover, the loss of HP2 function drastically altered auxin signaling in tomato fruits, resulting in higher activation of the auxin-responsive promoter DR5, severe down-regulation of AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) genes and altered accumulation of AUXIN RESPONSE FACTOR (ARF) transcripts. Both tomato ARF2 paralogues (Sl-ARF2a and SlARF2b) were up-regulated in hp2 fruits, which agrees with the promotive roles played by these ARFs in tomato fruit ripening and carotenoid biosynthesis. Among the genes differentially expressed in hp2 fruits, the additive effect of light treatment and loss of HP2 function was particularly evident for those encoding carotenoid biosynthetic enzymes, ethylene-related transcription factors, Aux/IAAs and ARFs. Altogether, the data uncover the involvement of ethylene and auxin as part of the light signaling cascades controlling tomato fruit metabolism and provide a new link between light signaling, plant hormone sensitivity and carotenoid metabolism in ripening fruits.

Recurrent water deficit causes epigenetic and hormonal changes in citrus plants

The present study evaluated the physiological, molecular and hormonal parameters from scion/rootstock interaction of citrus plants during recurrent water deficit. Responses of the Valencia (VO) scion variety grafted on two rootstocks with different soil water extraction capacities, Rangpur Lime (RL) and Sunki Maravilha (SM), during three successive periods of water deficit: plants exposed to a single episode of water deficit (WD1) and plants exposed to two (WD2) and three (WD3) recurrent periods of WD were compared. The combinations VO/RL and VO/SM presented polymorphic alterations of epigenetic marks and hormonal (i.e. abscisic acid, auxins and salicylicacid) profiles, which were particularly prominent when VO/SM plantswere exposed toWD3 treatment. Upon successive drought events, the VO/SM combination presented acclimatization characteristics that enable higher tolerance to water deficit by increasing transpiration (E), stomatal conductance (g _s ) and photosynthetic rate (A), which in turn may have facilitated the whole plant survival. Besides providing comprehensive data on the scion/rootstock interactions upon successive stress events, this study brings the first dataset suggesting that epigenetic alterations in citrus plants triggered by recurrent water deficit lead to improved drought tolerance in this crop species.

Differential accumulation of flavonoids and phytohormones resulting from the canopy/rootstock interaction of citrus plants subjected to dehydration/rehydration

Water scarcity can elicit drastic changes in plant metabolic and hormonal regulation, which may be of fundamental importance to stress tolerance. The study of plant the metabolic alterations in response to water deficit, especially the effects of the rootstocks level, is important to elucidate the mechanisms associated to drought tolerance. To verify the influence of rootstock and grafting on the tolerance to drought in citrus plants, we analyzed the growth, phytohormone levels and flavonoid profiles in grafted and ungrafted citrus plants subjected to different soil water regimes on plant status (well-watered, moderate drought and severe drought and rehydrated) under field conditions. The experiments were conducted under field conditions in the Brazilian Agricultural Research Corporation (EMBRAPA), Cruz das Almas, BA, Brazil. Water deficit reduced the total leaf area per plant in all canopy/rootstock combinations. Self-grafting reduce root volume, area and length when compared to ungrafted plants. Drought-induced increases in salicylic acid and abscisic acid associated with concomitant reductions in indoleacetic acid were observed in most canopy/rootstock combinations. However, plants with 'Sunki Maravilha' rootstocks exhibited the most pronounced changes in hormonal levels upon drought stress. Associated to these hormonal changes, drought also significantly affected flavonoid content and profile in both leaves and roots of the distinct citrus combinations. Glycosylated (GFs) and polimethoxylated flavonoids were predominantly found in leaves, whereas prenylated coumarins were found in the roots. Leaf levels of GFs (vicenin, F11, rutin and rhoifolin) were particularly modulated by drought in plants with 'Rangpur Santa Cruz' lime rootstock, whereas root levels of prenylated coumarins were most regulated by drought in plants with the 'Sunki Maravilha' root system. Taken together, these data indicate that the impacts of water deficit restriction on growth, hormonal balance and flavonoid profiles significantly varies depending on the canopy/rootstock combinations.

Manipulation of a Senescence-Associated Gene Improves Fleshy Fruit Yield

Senescence is the process that marks the end of a leaf's lifespan. As it progresses, the massive macromolecular catabolism dismantles the chloroplasts and, consequently, decreases the photosynthetic capacity of these organs. Thus, senescence manipulation is a strategy to improve plant yield by extending the leaf's photosynthetically active window of time. However, it remains to be addressed if this approach can improve fleshy fruit production and nutritional quality. One way to delay senescence initiation is by regulating key transcription factors (TFs) involved in triggering this process, such as the NAC TF ORESARA1 (ORE1). Here, three senescence-related NAC TFs from tomato (Solanum lycopersicum) were identified, namely SlORE1S02, SlORE1S03, and SlORE1S06. All three genes were shown to be responsive to senescence-inducing stimuli and posttranscriptionally regulated by the microRNA miR164 Moreover, the encoded proteins interacted physically with the chloroplast maintenance-related TF SlGLKs. This characterization led to the selection of a putative tomato ORE1 as target gene for RNA interference knockdown. Transgenic lines showed delayed senescence and enhanced carbon assimilation that, ultimately, increased the number of fruits and their total soluble solid content. Additionally, the fruit nutraceutical composition was enhanced. In conclusion, these data provide robust evidence that the manipulation of leaf senescence is an effective strategy for yield improvement in fleshy fruit-bearing species.

Phytochromobilin deficiency impairs sugar metabolism through the regulation of cytokinin and auxin signaling in tomato fruits

Phytochomes and plant hormones have been emerging as important regulators of fleshy fruit biology and quality traits; however, the relevance of phytochrome-hormonal signaling crosstalk in controlling fruit development and metabolism remains elusive. Here, we show that the deficiency in phytochrome chromophore phytochromobilin (PΦB) biosynthesis inhibits sugar accumulation in tomato (Solanum lycopersicum) fruits by transcriptionally downregulating sink- and starch biosynthesis-related enzymes, such as cell-wall invertases, sucrose transporters and ADP-glucose pyrophosphorylases. PΦB deficiency was also shown to repress fruit chloroplast biogenesis, which implicates more limited production of photoassimilates via fruit photosynthesis. Genetic and physiological data revealed the involvement of auxins and cytokinins in mediating the negative impact of PΦB deficiency on fruit sink strength and chloroplast formation. PΦB deficiency was shown to transcriptionally repress type-A TOMATO RESPONSE REGULATORs and AUXIN RESPONSE FACTORs both in pericarp and columella, suggesting active phytochrome-hormonal signaling crosstalk in these tissues. Data also revealed that PΦB deficiency influences fruit ripening by delaying the climacteric rise in ethylene production and signaling. Altogether, the data uncover the impact of phytochromobilin deficiency in fine-tuning sugar metabolism, chloroplast formation and the timing of fruit ripening and also reveal a link between auxins, cytokinins and phytochromes in regulating sugar import and accumulation in fruits.

Alternative fluorimetric-based method to detect and compare total S-nitrosothiols in plants

Nitric oxide (NO) is an important signaling molecule occurring in virtually all organisms, whose mechanism of action relies mainly on its interaction with proteins or peptides by nitrosylation, forming compounds such as S-nitrosothiols (SNO). The Saville reaction and the ozone-based chemiluminescence method are the main techniques used for nitrosylated protein quantification. While the Saville assay is not very sensitive, the ozone-based chemiluminescence is expensive and time-consuming. Here we propose a method in which the protein-bound NO groups are exposed to UV light, cleaving the bond and allowing the quantification of the derived NO molecules by diamino-rhodamine (DAR) dyes. The DAR-based method was shown to be specific in plant tissues by pre-treatment of the samples with reducing agents and parallel EPR analysis. Spike-and-recovery assays revealed 72% recovery after a GSNO spike. Moreover, the method was significantly more sensitive than the Saville reaction, and this increase in sensitivity was crucial for detecting the reduced levels of nitrosylated proteins in plant species other than Arabidopsis. The method presented here is a suitable alternative to compare plant samples, allowing simple and fast detection of nitrosylated proteins.

Shedding light on NO homeostasis: Light as a key regulator of glutathione and nitric oxide metabolisms during seedling deetiolation

Despite the significant impacts of light on nitric oxide (NO) levels in plants, the mechanism underlying the influence of this environmental factor on NO metabolism remains poorly understood. A critical mechanism controlling NO levels in plant cells relies on the S-nitrosylation of glutathione (GSH), giving rise to S-nitrosoglutathione (GSNO), which can be either stored or degraded depending on the cellular context. Here, we demonstrate that a strict balance is maintained between NO generation and scavenging during tomato (Solanum lycopersicum) seedling deetiolation. Given the absence of accurate methods in the literature to estimate NO scavenging in planta, we first developed a simple, robust system to continuously monitor the global in vivo NO scavenging by plant tissues. Then, using photomorphogenic tomato mutants, we demonstrated that the light-evoked de-etiolation is associated with a dramatic rise in NO content followed by a progressive increment in NO scavenging capacity of the tissues. Light-driven increments in NO scavenging rates coincided with pronounced rises in S-nitrosothiol content and GSNO reductase (GSNOR) activity, thereby suggesting that GSNO formation and subsequent removal via GSNOR might be key for controlling NO levels during seedling deetiolation. Accordingly, treatments with thiol-blocking compounds further indicated that thiol nitrosylation might be critically involved in the NO scavenging mechanism responsible for maintaining NO homeostasis during deetiolation. The impacts of both light and NO on the transcriptional profile of glutathione metabolic genes also revealed an independent but coordinated action of these signals on the regulation of key components of glutathione and GSNO metabolisms. Altogether, these data indicated that GSNO formation and subsequent removal might facilitate maintaining NO homeostasis during light-driven seedling deetiolation.

Nitric oxide signaling and its crosstalk with other plant growth regulators in plant responses to abiotic stress

Nitric oxide (NO) is a free radical molecule involved in an array of functions under physiological and adverse environmental conditions. As other free radical molecules, NO biological action depends on its cellular concentration, acting as a signal molecule when produced at low concentration or resulting in cellular damage when produced at sufficiently high levels to trigger nitro-oxidative stress. Over the last decade, significant progress has been made in characterizing NO metabolism and action mechanism, revealing that diverse biosynthetic routes can generate this free radical in plants and its action mainly occurs through posttranslational modification (nitration and S-nitrosylation) of target proteins. Intricate crosstalk networks between NO and other signaling molecules have been described involving phytohormones, other second messengers, and key transcription factors. This review will focus on our current understanding of NO interplay with phytohormones and other plant growth regulators under abiotic stress conditions.

Survival strategies of citrus rootstocks subjected to drought

Two citrus rootstocks, Rangpur lime (RL) and Sunki Maravilha mandarin (SM), were analyzed either ungrafted or grafted with their reciprocal graft combinations or with shoot scions of two commercial citrus varieties: Valencia orange (VO) and Tahiti acid lime (TAL). All graft combinations were subjected to distinct watering regimes: well-watered, severe drought and rehydration. Growth and water relation parameters, gas exchange as well as sugar and hormone profiles were determined. Data indicated that RL adopted a dehydration avoidance strategy and maintained growth, whereas SM adopted a dehydration tolerance strategy focused on plant survival. Compared with RL, the leaves and roots of SM exhibited higher concentrations of abscisic acid and salicylic acid, which induced drought tolerance, and accumulation of carbohydrates such as trehalose and raffinose, which are important reactive oxygen species scavengers. SM rootstocks were able to transfer their survival strategy to the grafted shoot scions (RL, VO, TAL). Because of their contrasting survival strategies, RL reached the permanent wilting point more quickly than SM whereas SM recovered from prolonged droughts more efficiently than RL. This is one of the most complete studies of drought tolerance mechanisms in citrus crops and is the first to use reciprocal grafting to clarify scion/rootstock interactions.

Phytochrome Interacting Factors (PIFs) in Solanum lycopersicum: Diversity, Evolutionary History and Expression Profiling during Different Developmental Processes

Although the importance of light for tomato plant yield and edible fruit quality is well known, the PHYTOCHROME INTERACTING FACTORS (PIFs), main components of phytochrome-mediated light signal transduction, have been studied almost exclusively in Arabidopsis thaliana. Here, the diversity, evolution and expression profile of PIF gene subfamily in Solanum lycopersicum was characterized. Eight tomato PIF loci were identified, named SlPIF1a, SlPIF1b, SlPIF3, SlPIF4, SlPIF7a, SlPIF7b, SlPIF8a and SlPIF8b. The duplication of SlPIF1, SlPIF7 and SlPIF8 genes were dated and temporally coincided with the whole-genome triplication event that preceded tomato and potato divergence. Different patterns of mRNA accumulation in response to light treatments were observed during seedling deetiolation, dark-induced senescence, diel cycle and fruit ripening. SlPIF4 showed similar expression profile as that reported for A. thaliana homologs, indicating an evolutionary conserved function of PIF4 clade. A comprehensive analysis of the evolutionary and transcriptional data allowed proposing that duplicated SlPIFs have undergone sub- and neofunctionalization at mRNA level, pinpointing the importance of transcriptional regulation for the maintenance of duplicated genes. Altogether, the results indicate that genome polyploidization and functional divergence have played a major role in diversification of the Solanum PIF gene subfamily.

Nitric Oxide, Ethylene, and Auxin Cross Talk Mediates Greening and Plastid Development in Deetiolating Tomato Seedlings

The transition from etiolated to green seedlings involves the conversion of etioplasts into mature chloroplasts via a multifaceted, light-driven process comprising multiple, tightly coordinated signaling networks. Here, we demonstrate that light-induced greening and chloroplast differentiation in tomato (Solanum lycopersicum) seedlings are mediated by an intricate cross talk among phytochromes, nitric oxide (NO), ethylene, and auxins. Genetic and pharmacological evidence indicated that either endogenously produced or exogenously applied NO promotes seedling greening by repressing ethylene biosynthesis and inducing auxin accumulation in tomato cotyledons. Analysis performed in hormonal tomato mutants also demonstrated that NO production itself is negatively and positively regulated by ethylene and auxins, respectively. Representing a major biosynthetic source of NO in tomato cotyledons, nitrate reductase was shown to be under strict control of both phytochrome and hormonal signals. A close NO-phytochrome interaction was revealed by the almost complete recovery of the etiolated phenotype of red light-grown seedlings of the tomato phytochrome-deficient aurea mutant upon NO fumigation. In this mutant, NO supplementation induced cotyledon greening, chloroplast differentiation, and hormonal and gene expression alterations similar to those detected in light-exposed wild-type seedlings. NO negatively impacted the transcript accumulation of genes encoding phytochromes, photomorphogenesis-repressor factors, and plastid division proteins, revealing that this free radical can mimic transcriptional changes typically triggered by phytochrome-dependent light perception. Therefore, our data indicate that negative and positive regulatory feedback loops orchestrate ethylene-NO and auxin-NO interactions, respectively, during the conversion of colorless etiolated seedlings into green, photosynthetically competent young plants.