Integrated Analysis of the Transcriptome and Metabolomics Reveals an Essential Role for Auxin in Hypocotyl Elongation During End-of-Day Far-Red Treatment of Cucurbita Moschata

Abstract BackgroundLong, robust hypocotyls are important for facilitating greenhouse transplant production. Use of far-red light at the end of the day (end-of-day far-red, EOD-FR) is known to affect hypocotyl elongation. Auxin is an important regulator of plant growth and development, but its role and mechanism in EOD-FR-mediated hypocotyl elongation remain unclear. Here we combined transcriptome sequencing and metabolite profiling of pumpkin hypocotyls with related physiological experiments to provide insight into the mechanisms by which auxin affects the response to EOD-FR. ResultsAfter EOD-FR treatment, the length of pumpkin Hypocotyl and the IAA level of plant Hypocotyl were significantly promoted. When NPA was applied, the Hypocotyl elongation mediated by EOD-FR and the increase of IAA content were counteracted.At the same time, through the observation of Hypocotyl sections, we found that hypocotyl cells expanded significantly after EOD-FR treatment.After EOD-FR treatment, 2801 DEGs, were identified in hypocotyl, of which 31 DEGs related to auxin synthesis, transport and signal transduction and 25 cell wall protein genes were identified.Through the detection of metabolic group, it was found that the levels of tryptophan and indole in plant increased after EOD-FR treatment.All these indicate that auxin plays an essential role in EOD-FR-mediated hypocotyl elongation.ConclusionsWe identified a large number of differentially expressed genes related to auxin synthesis, transport, and downstream response. We speculate that auxin is essential for pumpkin hypocotyl elongation mediated by EOD-FR, and that the synthesis of free IAA may be performed by the tryptophan-dependent TAA-YUC pathway. This study improves our understanding of auxin’s role in EOD-FR-mediated hypocotyl elongation.

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Integrated Transcriptome and Metabolome Analysis Reveals an Essential Role for Auxin in Hypocotyl Elongation during End-of-Day Far-Red Treatment of Cucurbita moschata (Duch. Ex Lam.)

Agronomy ◽

10.3390/agronomy11050853 ◽

2021 ◽

Vol 11 (5) ◽

pp. 853

Author(s):

Qi Liu ◽

Hanqing Zhang ◽

Yanhao Mei ◽

Qi Li ◽

Yahui Bai ◽

...

Keyword(s):

Essential Role ◽

Parenchymal Cell ◽

Red Light ◽

Hypocotyl Elongation ◽

Metabolome Analysis ◽

Hypocotyl Length ◽

Transport Inhibitor ◽

Auxin Transport Inhibitor ◽

Naphthylphthalamic Acid ◽

Shed Light

Long, robust hypocotyls are important for facilitating greenhouse transplant production. The use of far-red light at the end of the day (end-of-day far-red, EOD-FR) is known to prompt hypocotyl elongation, but the mechanism of EOD-FR-mediated hypocotyl elongation in pumpkin remains unclear. Here, we found that hypocotyl length, parenchymal cell size in hypocotyls, and plant IAA levels were significantly greater in pumpkin after EOD-FR treatment. This effect was counteracted by the application of the polar auxin transport inhibitor 1-N-naphthylphthalamic acid. Integrated transcriptomic and metabolomic analysis of pumpkin hypocotyls revealed that the expression of auxin-related genes changed significantly after EOD-FR treatment, and the contents of the auxin biosynthetic precursors tryptophan and indole were also significantly higher. Our results show that auxin plays an essential role in EOD-FR-mediated hypocotyl elongation, shed light on the mechanisms of EOD-FR mediated hypocotyl elongation, and provide a theoretical basis for the use of EOD-FR in facility cultivation.

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Guard cells control hypocotyl elongation through HXK1, HY5, and PIF4

Communications Biology ◽

10.1038/s42003-021-02283-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Gilor Kelly ◽

Danja Brandsma ◽

Aiman Egbaria ◽

Ofer Stein ◽

Adi Doron-Faigenboim ◽

...

Keyword(s):

Transcription Factors ◽

Blue Light ◽

Opposite Effect ◽

Red Light ◽

Guard Cells ◽

Cell Types ◽

Hypocotyl Elongation ◽

Sugar Production ◽

Effect Of Light

AbstractThe hypocotyls of germinating seedlings elongate in a search for light to enable autotrophic sugar production. Upon exposure to light, photoreceptors that are activated by blue and red light halt elongation by preventing the degradation of the hypocotyl-elongation inhibitor HY5 and by inhibiting the activity of the elongation-promoting transcription factors PIFs. The question of how sugar affects hypocotyl elongation and which cell types stimulate and stop that elongation remains unresolved. We found that overexpression of a sugar sensor, Arabidopsis hexokinase 1 (HXK1), in guard cells promotes hypocotyl elongation under white and blue light through PIF4. Furthermore, expression of PIF4 in guard cells is sufficient to promote hypocotyl elongation in the light, while expression of HY5 in guard cells is sufficient to inhibit the elongation of the hy5 mutant and the elongation stimulated by HXK1. HY5 exits the guard cells and inhibits hypocotyl elongation, but is degraded in the dark. We also show that the inhibition of hypocotyl elongation by guard cells’ HY5 involves auto-activation of HY5 expression in other tissues. It appears that guard cells are capable of coordinating hypocotyl elongation and that sugar and HXK1 have the opposite effect of light on hypocotyl elongation, converging at PIF4.

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Insight into the practical models for prediciting the essential role of the cytochrome P450-mediated biotransformation in emodin-associated hepatotoxicity

Toxicology ◽

10.1016/j.tox.2021.152930 ◽

2021 ◽

Vol 462 ◽

pp. 152930

Author(s):

Tingting Zhang ◽

Xiaomei He ◽

Lanlan Sun ◽

Dong Wang ◽

Shuya Zhang ◽

...

Keyword(s):

Cytochrome P450 ◽

Essential Role ◽

Insight Into

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N-1-naphthylphthalamic acid stimulates tomato hypocotyl elongation, elevates ethylene levels and alters metabolic homeostasis

10.1101/311159 ◽

2018 ◽

Author(s):

Sapana Nongmaithem ◽

Sameera Devulapalli ◽

Yellamaraju Sreelakshmi ◽

Rameshwar Sharma

Keyword(s):

Butyric Acid ◽

Metabolic Networks ◽

Higher Plants ◽

Red Light ◽

Hypocotyl Elongation ◽

Stimulated Emission ◽

Ethylene Action ◽

Naphthylphthalamic Acid ◽

Exogenous Ethylene ◽

Species Specific

One sentence summaryN-1-naphthylphthalamic acid (NPA) treatment stimulates tomato hypocotyl elongation likely by elevating ethylene emission and lowering indole-3-butyric acid levels in the seedlings.AbstractIn higher plants, phytohormone indole-3-acetic acid is characteristically transported from the apex towards the base of the plant, termed as polar auxin transport (PAT). Among the inhibitors blocking PAT, N-1-naphthylphthalamic acid (NPA) that targets ABCB transporters is most commonly used. NPA-treated light-grown Arabidopsis seedlings show severe inhibition of hypocotyl and root elongation. In light-grown tomato seedlings, NPA inhibited root growth, but contrary to Arabidopsis stimulated hypocotyl elongation. The NPA-stimulation of hypocotyl elongation was milder in blue, red, and far-red light-grown seedlings. The NPA-treatment stimulated emission of ethylene from the seedlings. The scrubbing of ethylene by mercuric perchlorate reduced NPA-stimulated hypocotyl elongation. NPA action on hypocotyl elongation was antagonized by 1-methylcyclopropene, an inhibitor of ethylene action. NPA-treated seedlings had reduced levels of indole-3-butyric acid and higher levels of zeatin in the shoots. NPA did not alter indole-3-acetic levels in shoots. The analysis of metabolic networks indicated that NPA-treatment induced moderate shifts in the networks compared to exogenous ethylene that induced a drastic shift in metabolic networks. Our results indicate that in addition to ethylene, NPA-stimulated hypocotyl elongation in tomato may also involve zeatin and indole-3-butyric acid. Our results indicate that NPA-mediated physiological responses may vary in a species-specific fashion.

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Overview of neuroimaging

Oxford Textbook of Neurological Surgery ◽

10.1093/med/9780198746706.003.0003 ◽

2019 ◽

pp. 31-44

Author(s):

Tomasz Matys ◽

Daniel. J. Scoffings ◽

Tilak Das

Keyword(s):

Essential Role ◽

Imaging Techniques ◽

Disease Process ◽

Future Directions ◽

Anatomical Imaging ◽

Radiological Methods ◽

Physical Principles ◽

Insight Into ◽

Individual Disease

Imaging plays an essential role in the diagnosis and treatment of neurosurgical conditions. This chapter discusses the basic physical principles, applications, and limitations of the main imaging techniques used in neurosurgical practice, and highlights potential future directions of functional and molecular neuroimaging. Current conventional radiological methods allow demonstration of anatomical and macroscopic pathological features of disease with excellent sensitivity and resolution. Functional imaging methods that have enabled insight into a variety of physiological and pathological phenomena are also described, and are an important first step beyond anatomical imaging towards more precise characterization of the disease process. These methods however remain generally non-specific, demonstrating changes that are common endpoints of many possible pathological pathways. This chapter also covers current neuroradiology imaging modalities that are useful in neurosurgical practice, and focuses on the general usefulness and limitations of neuroradiological methods rather than the imaging manifestations of individual disease processes, which are discussed elsewhere in this book.

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Interactive Effects of Light Quality and Temperature on Arabidopsis Growth and Immunity

Plant and Cell Physiology ◽

10.1093/pcp/pcaa020 ◽

2020 ◽

Vol 61 (5) ◽

pp. 933-941

Author(s):

Xiaoying Liu ◽

Chunmei Xue ◽

Le Kong ◽

Ruining Li ◽

Zhigang Xu ◽

...

Keyword(s):

Disease Resistance ◽

Blue Light ◽

Light Quality ◽

Red Light ◽

Complex Interaction ◽

Hypocotyl Elongation ◽

Interactive Effects ◽

Phytochrome B ◽

Light Conditions ◽

Effects Of Temperature

Abstract We report here the interactive effects of three light qualities (white, red and blue) and three growth temperatures (16�C, 22�C and 28�C) on rosette growth, hypocotyl elongation and disease resistance in Arabidopsis thaliana. While an increase in temperature promotes hypocotyl elongation irrespective of light quality, the effects of temperature on rosette growth and disease resistance are dependent on light quality. Maximum rosette growth rate under white, red and blue light are observed at 28�C, 16�C and 22�C, respectively. The highest disease resistance is observed at 16�C under all three light conditions, but the highest susceptibility is observed at 28�C for white light and 22�C for red and blue light. Interestingly, rosette growth is inhibited by phytochrome B (PHYB) under blue light at 28�C and by cryptochromes (CRYs) under red light at 16�C. In addition, disease resistance is inhibited by PHYB under blue light and promoted by CRYs under red light. Therefore, this study reveals a complex interaction between light and temperature in modulating rosette growth and disease resistance as well as the contribution of PHYB and CRY to disease resistance.

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Insight into transketolase of Pyropia haitanensis under desiccation stress based on integrative analysis of omics and transformation

BMC Plant Biology ◽

10.1186/s12870-019-2076-4 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Jianzhi Shi ◽

Wenlei Wang ◽

Yinghui Lin ◽

Kai Xu ◽

Yan Xu ◽

...

Keyword(s):

Desiccation Tolerance ◽

Integrative Analysis ◽

Pyropia Haitanensis ◽

Desiccation Stress ◽

Integrated Analysis ◽

Antioxidant Systems ◽

Water Losses ◽

Harsh Conditions ◽

Insight Into ◽

Better Than

Abstract Background Pyropia haitanensis, distributes in the intertidal zone, can tolerate water losses exceeding 90%. However, the mechanisms enabling P. haitanensis to survive harsh conditions remain uncharacterized. To elucidate the mechanism underlying P. haitanensis desiccation tolerance, we completed an integrated analysis of its transcriptome and proteome as well as transgenic Chlamydomonas reinhardtii carrying a P. haitanensis gene. Results P. haitanensis rapidly adjusted its physiological activities to compensate for water losses up to 60%, after which, photosynthesis, antioxidant systems, chaperones, and cytoskeleton were activated to response to severe desiccation stress. The integrative analysis suggested that transketolase (TKL) was affected by all desiccation treatments. Transgenic C. reinhardtii cells overexpressed PhTKL grew better than the wild-type cells in response to osmotic stress. Conclusion P. haitanensis quickly establishes acclimatory homeostasis regarding its transcriptome and proteome to ensure its thalli can recover after being rehydrated. Additionally, PhTKL is vital for P. haitanensis desiccation tolerance. The present data may provide new insights for the breeding of algae and plants exhibiting enhanced desiccation tolerance.

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Deconstructing and repurposing the light-regulated interplay between Arabidopsis phytochromes and interacting factors

Communications Biology ◽

10.1038/s42003-019-0687-9 ◽

2019 ◽

Vol 2 (1) ◽

Cited By ~ 4

Author(s):

David Golonka ◽

Patrick Fischbach ◽

Siddhartha G. Jena ◽

Julius R. W. Kleeberg ◽

Lars-Oliver Essen ◽

...

Keyword(s):

Mammalian Cells ◽

Red Light ◽

Interaction Data ◽

Phytochrome B ◽

Adaptive Responses ◽

Membrane Recruitment ◽

C Terminus ◽

Regulated Gene Expression ◽

Insight Into ◽

Differential Affinity

AbstractPhytochrome photoreceptors mediate adaptive responses of plants to red and far-red light. These responses generally entail light-regulated association between phytochromes and other proteins, among them the phytochrome-interacting factors (PIF). The interaction with Arabidopsis thaliana phytochrome B (AtPhyB) localizes to the bipartite APB motif of the A. thaliana PIFs (AtPIF). To address a dearth of quantitative interaction data, we construct and analyze numerous AtPIF3/6 variants. Red-light-activated binding is predominantly mediated by the APB N-terminus, whereas the C-terminus modulates binding and underlies the differential affinity of AtPIF3 and AtPIF6. We identify AtPIF variants of reduced size, monomeric or homodimeric state, and with AtPhyB affinities between 10 and 700 nM. Optogenetically deployed in mammalian cells, the AtPIF variants drive light-regulated gene expression and membrane recruitment, in certain cases reducing basal activity and enhancing regulatory response. Moreover, our results provide hitherto unavailable quantitative insight into the AtPhyB:AtPIF interaction underpinning vital light-dependent responses in plants.

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Differential effects of insulin-like growth factors I and II on growth, differentiation and glucoregulation in differentiating chondrocyte cells in culture

Acta Endocrinologica ◽

10.1530/acta.0.1250201 ◽

1991 ◽

Vol 125 (2) ◽

pp. 201-211 ◽

Cited By ~ 35

Author(s):

Banani Bhaumick ◽

R. Marvin Bala

Keyword(s):

Growth Factors ◽

Limb Bud ◽

Previous Suggestion ◽

Limb Buds ◽

Differentiated Cells ◽

Igf I ◽

Embryonic Limb ◽

Important Regulator ◽

Insight Into ◽

Insulin Like Growth Factors

Abstract. Insulin-like growth factors I and II have been shown differentially to affect the growth and carbohydrate metabolism of differentiating cartilage developed from mouse embryonic limb buds in organ culture. To gain insight into the relative importance of IGF-I and II actions in different stages of development of cartilage we have established a primary culture of differentiating chondrocytes from mouse embryonic limb buds. Trypsin digested limb bud cells from 9-11 day old mouse embryos differentiated into chondrocytes by 5-7 days in culture. At all stages of differentiation, distinct receptors of IGF-I and II were observed. IGF-I stimulated growth and sulphate incorporation of the non-differentiated and differentiated chondrocytes. IGF-II stimulated growth of the non-differentiated cells and had no effect on growth or sulphate incorporation by the differentiated cells. IGF-II, however, stimulated the glucose uptake by the cells at all stages of differentiation. These data confirm our previous suggestion that IGF-I in cartilage is the regulator of growth and differentiation, while IGF-II may be an important regulator of glucose metabolism in the tissue.

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