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.Fil: Bianchetti, Ricardo. Universidade de Sao Paulo; BrasilFil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: de Haro, Luis Alejandro. Weizmann Institute Of Science Israel; Israel. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zuccarelli, Rafael. Universidade de Sao Paulo; BrasilFil: Rosado, Daniele. Universidade de Sao Paulo; BrasilFil: Freschi, Luciano. Universidade de Sao Paulo; BrasilFil: Rossi, Magdalena. Universidade de Sao Paulo; BrasilFil: Bermudez Salazar, Luisa Fernanda. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentin

Plant degreening: evolution and expression of tomato\ud (Solanum lycopersicum) dephytylation enzymes

Chlorophyll is the most abundant pigment on earth and even though it is known that its high photo-excitability necessitates a tight regulation of its degradation pathway, to date there are still several steps in chlorophyll breakdown that remain obscure. In order to better understand the ‘degreening’ processes that accompany leaf senescence and fruit ripening, we characterized the enzyme-encoding genes involved in dephytylation from tomato (Solanum lycopersicum). A single pheophytinase (PPH) gene and four chlorophyllase (CLH) genes were identified in the tomato genome. A phenetic analysis revealed two groups of CLHs in eudicot species and further evolutionary analysis indicated that these enzymes are under diverse selection pressures. A comprehensive expression profile analysis also suggested functional specificity for these dephytylating enzymes. The integrated analysis allows us to propose three general roles for chlorophyll dephytylation: i) PPH, which is under high selective constraint, is responsible for chlorophyll degradation during developmentally programed physiological processes; ii) Group I CLHs, which are under relaxed selection constraint, respond to environmental and hormonal stimuli and play a role in plant adaptation plasticity; and iii) Group II CLHs, which are also under high selective constraint, are mostly involved in chlorophyll recycling.BSL and JA were recipients of FAPESP fellowships and MR was funded by a fellowship from CNPq. This work was supported by FAPESP2012-12531-8 (Brazil). The authors thank Rohm and Haas Company for generous donation of the 1-methylcyclopropene (SmartFresh®) used for the experiments

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.This work was supported by the São Paulo Research Foundation (FAPESP) (grants 2018/16389-8, 2016/04924-0, 2017/17935-3 and 2016/01128-9), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) (grants 422287/2018-0, 305012/2018-5, 303332/2019-0 and 300986/2018-1), and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. The research work of FJC and JMP is supported by a European Regional Development Fund cofinanced grant from the Ministry of Economy and Competitiveness (AGL2015-65104-P and PID2019-103924GB-I00), Spain

Ethylene Modulates the Developmental Plasticity and the Growth Balance Between Shoot and Root Systems in the In Vitro Grown Epiphytic Orchid Catasetum fimbriatum

The epiphytic habitat is potentially one of the most stressful environments for plants, making the effective developmental control in response to external cues critical for epiphyte survival. Because ethylene mediates several abiotic stresses in plants, here, we have examined the ethylene influence in both shoot and root systems of the epiphytic orchid Catasetum fimbriatum. Under controlled conditions, ethylene production was quantified during an entire growth cycle of C. fimbriatum development in vitro, while treatments modulating either ethylene concentration or perception were carried out over the early growth phase of these plants. After treatments, growth measurements and histological features were studied in both shoot and root tissues. Ethylene production showed a decreasing trend over the period of organ elongation; however, it increased considerably when leaves were shed, and a new axillary bud was initiating. The early exposure of young plants to higher concentrations of ethylene triggered morphogenic responses that included root hair formation instead of velamen, and a combination of inhibitory effects (decreases in both stem enlargement and cellular/organ elongation) and inductive effects (increases in leaf and root formation, bud initiation and cellular thickening) on plant growth, which favored biomass allocation to roots. Conversely, inhibition of ethylene perception over the plant growth phase generally resulted in the opposite morphogenic responses. Our data indicate that periodic variations in ethylene concentration and/or sensitivity seem to modulate several developmental features in shoot and root systems of C. fimbriatum which could have adaptive significance during the growing phase of this epiphytic orchid.The authors thank Rohm and Haas Co. for a generous donation of the 1-methylcyclopropene (SmartFresh®), the inhibitor of ethylene perception used in several experiments presented in this article. This study was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) through financial assistance to the Laboratory of Plant Physiology – IBUSP (Grant No. 04/08049–0 to GBK) and a PhD fellowship to MA Rodrigues (No. 04/08891–2)

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

Auxin production by the plant trypanosomatid Phytomonas\ud serpens and auxin homoeostasis in infected tomato fruits

Previously we have characterized the complete gene encoding a pyruvate decarboxylase (PDC)/indolepyruvate\ud decarboxylase (IPDC) of Phytomonas serpens, a trypanosomatid highly abundant in tomato fruits. Phylogenetic analyses\ud indicated that the clade that contains the trypanosomatid protein behaves as a sister group of IPDCs of γ-proteobacteria.\ud Since IPDCs are key enzymes in the biosynthesis of the plant hormone indole-3-acetic acid (IAA), the ability for IAA\ud production by P. serpens was investigated. Similar to many microorganisms, the production of IAA and related indolic\ud compounds, quantified by high performance liquid chromatography, increased inP. serpens media in response to amounts\ud of tryptophan. The auxin functionality was confirmed in the hypocotyl elongation assay. In tomato fruits inoculated with\ud P. serpensthe concentration of free IAA had no significant variation, whereas increased levels of IAA-amide and IAA-ester\ud conjugates were observed. The data suggest that the auxin produced by the flagellate is converted to IAA conjugates,\ud keeping unaltered the concentration of free IAA. Ethanol also accumulated inP. serpens-conditioned media, as the result of\ud a PDC activity. In the article we discuss the hypothesis of the bifunctionality of P. serpens PDC/IPDC and provide a\ud three-dimensional model of the enzyme.FAPESP) (grant number 2010/50957-1)(CNPq) (grant number 304793/2009-4)FAPESP (grant number 2008/50209-5

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