Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply

AbstractThe biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with 67Zn isotope revealed whole plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1893 zinc-responsive genes. Multiple ZIP transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.

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Slc39a1 to 3 (subfamily II) Zip genes in mice have unique cell-specific functions during adaptation to zinc deficiency

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00130.2008 ◽

2008 ◽

Vol 294 (5) ◽

pp. R1474-R1481 ◽

Cited By ~ 40

Author(s):

Taiho Kambe ◽

Jim Geiser ◽

Brett Lahner ◽

David E. Salt ◽

Glen K. Andrews

Keyword(s):

Alkaline Phosphatase ◽

Phosphatase Activity ◽

Zinc Deficiency ◽

Alkaline Phosphatase Activity ◽

Knockout Mice ◽

Targeted Mutagenesis ◽

Zinc Homeostasis ◽

Wild Type ◽

Liver And Pancreas ◽

Zip Genes

Subfamily II of the solute carrier (Slc)39a family contains three highly conserved members (ZIPs 1–3) that share a 12-amino acid signature sequence present in the putative fourth transmembrane domain and function as zinc transporters in transfected cells. The physiological significance of this genetic redundancy is unknown. Here we report that the complete elimination of all three of these Zip genes, by targeted mutagenesis and crossbreeding mice, causes no overt phenotypic effect. When mice were fed a zinc-adequate diet, several indicators of zinc status were indistinguishable between wild-type and triple-knockout mice, including embryonic morphogenesis and growth, alkaline phosphatase activity in the embryo, ZIP4 protein in the visceral yolk sac, and initial rates (30 min) of accumulation/retention of 67Zn in liver and pancreas. When mice were fed a zinc-deficient diet, embryonic membrane-bound alkaline phosphatase activity was reduced to a much greater extent, and 80% of the embryos of the triple-knockout mice developed abnormally compared with 12% of the embryos of wild-type mice. During zinc deficiency, the accumulation/retention (3 h) of 67Zn in the liver and pancreas of weanlings was significantly impaired in the triple-knockout mice compared with wild-type mice. Thus none of these three mammalian Zip genes apparently plays a critical role in zinc homeostasis when zinc is replete, but they play important, noncompensatory roles when this metal is deficient.

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Strigolactones and their crosstalk with other phytohormones

Annals of Botany ◽

10.1093/aob/mcz100 ◽

2019 ◽

Vol 124 (5) ◽

pp. 749-767 ◽

Cited By ~ 8

Author(s):

L O Omoarelojie ◽

M G Kulkarni ◽

J F Finnie ◽

J Van Staden

Keyword(s):

Salicylic Acid ◽

Abscisic Acid ◽

Plant Responses ◽

Research Attention ◽

Molecular Events ◽

Whole Plant ◽

Shoot Architecture ◽

Hormonal Crosstalk ◽

Morphological Processes ◽

Parasitic Interactions

Abstract Background Strigolactones (SLs) are a diverse class of butenolide-bearing phytohormones derived from the catabolism of carotenoids. They are associated with an increasing number of emerging regulatory roles in plant growth and development, including seed germination, root and shoot architecture patterning, nutrient acquisition, symbiotic and parasitic interactions, as well as mediation of plant responses to abiotic and biotic cues. Scope Here, we provide a concise overview of SL biosynthesis, signal transduction pathways and SL-mediated plant responses with a detailed discourse on the crosstalk(s) that exist between SLs/components of SL signalling and other phytohormones such as auxins, cytokinins, gibberellins, abscisic acid, ethylene, jasmonates and salicylic acid. Conclusion SLs elicit their control on physiological and morphological processes via a direct or indirect influence on the activities of other hormones and/or integrants of signalling cascades of other growth regulators. These, among many others, include modulation of hormone content, transport and distribution within plant tissues, interference with or complete dependence on downstream signal components of other phytohormones, as well as acting synergistically or antagonistically with other hormones to elicit plant responses. Although much has been done to evince the effects of SL interactions with other hormones at the cell and whole plant levels, research attention must be channelled towards elucidating the precise molecular events that underlie these processes. More especially in the case of abscisic acid, cytokinins, gibberellin, jasmonates and salicylic acid for which very little has been reported about their hormonal crosstalk with SLs.

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RNA-Seq Analysis of the Effect of Zinc Deficiency on Microsporum canis, ZafA Gene Is Important for Growth and Pathogenicity

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.727665 ◽

2021 ◽

Vol 11 ◽

Author(s):

Pengxiu Dai ◽

Yangou Lv ◽

Xiaowen Gong ◽

Jianye Han ◽

Peng Gao ◽

...

Keyword(s):

Gene Expression ◽

Zinc Deficiency ◽

Metabolic Pathway ◽

Gene Knockout ◽

Absorption Capacity ◽

Zinc Homeostasis ◽

Microsporum Canis ◽

Zinc Absorption ◽

Rna Seq

Microsporum canis, a common pathogenic skin fungus, can cause dermatophytosis in humans and animals. Zinc is an important trace element and plays an important role in the growth and metabolism of fungi. Currently, the effects of zinc deficiency on growth, gene expression, and metabolic pathway have not been clarified in M. canis. Therefore, M. canis was cultured under zinc restriction, and RNA-Seq was conducted in this study. The growth of M. canis was severely inhibited, and many genes showed significant upregulation and downregulation in M. canis with zinc deficiency. Zinc deficiency could negatively affect the gene expression and biological metabolic pathway in M. canis. The zinc-responsiveness transcriptional activator (ZafA) gene was significantly upregulated and shared homology with Zap1. Thus, the ZafA gene might be the main transcription factor regulating M. canis zinc homeostasis. The ZafA gene knockout strain, ZafA-hph, was constructed via Agrobacterium tumefaciens-mediated transformation (ATMT) in M. canis for the first time to assess its function. In vitro growth ability, hair biodegradation ability, virulence test, and zinc absorption capacity in ZafA-hph and wild-type M. canis strains were compared. Results showed that the ZafA gene plays an important role in zinc absorption, expression of zinc transporter genes, and growth and pathogenicity in M. canis and can be used as a new drug target. Cutting off the zinc absorption pathway can be used as a way to prevent and control infection in M. canis.

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RNA-Seq Provides New Insights into the Molecular Events Involved in “Ball-Skin versus Bladder Effect” on Fruit Cracking in Litchi

International Journal of Molecular Sciences ◽

10.3390/ijms22010454 ◽

2021 ◽

Vol 22 (1) ◽

pp. 454

Author(s):

Jun Wang ◽

Xiao Fang Wu ◽

Yong Tang ◽

Jian Guo Li ◽

Ming Lei Zhao

Keyword(s):

Transcription Factors ◽

Plant Hormones ◽

Fruit Development ◽

Economic Value ◽

Lipid Synthesis ◽

Expression Level ◽

Agricultural Product ◽

Rna Seq ◽

Fruit Cracking ◽

Molecular Events

Fruit cracking is a disorder of fruit development in response to internal or external cues, which causes a loss in the economic value of fruit. Therefore, exploring the mechanism underlying fruit cracking is of great significance to increase the economic yield of fruit trees. However, the molecular mechanism underlying fruit cracking is still poorly understood. Litchi, as an important tropical and subtropical fruit crop, contributes significantly to the gross agricultural product in Southeast Asia. One important agricultural concern in the litchi industry is that some famous varieties with high economic value such as ‘Nuomici’ are susceptible to fruit cracking. Here, the cracking-susceptible cultivar ‘Nuomici’ and cracking-resistant cultivar ‘Huaizhi’ were selected, and the samples including pericarp and aril during fruit development and cracking were collected for RNA-Seq analysis. Based on weighted gene co-expression network analysis (WGCNA) and the “ball-skin versus bladder effect” theory (fruit cracking occurs upon the aril expanding pressure exceeds the pericarp strength), it was found that seven co-expression modules genes (1733 candidate genes) were closely associated with fruit cracking in ‘Nuomici’. Importantly, we propose that the low expression level of genes related to plant hormones (Auxin, Gibberellins, Ethylene), transcription factors, calcium transport and signaling, and lipid synthesis might decrease the mechanical strength of pericarp in ‘Nuomici’, while high expression level of genes associated with plant hormones (Auxin and abscisic acid), transcription factors, starch/sucrose metabolism, and sugar/water transport might increase the aril expanding pressure, thereby resulting in fruit cracking in ‘Nuomici’. In conclusion, our results provide comprehensive molecular events involved in the “ball-skin versus bladder effect” on fruit cracking in litchi.

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Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply

Plant Cell & Environment ◽

10.1111/pce.14151 ◽

2021 ◽

Author(s):

Sahand Amini ◽

Borjana Arsova ◽

Sylvie Gobert ◽

Monique Carnol ◽

Bernard Bosman ◽

...

Keyword(s):

Transcriptional Regulation ◽

Zinc Deficiency ◽

Zinc Status ◽

Zip Genes

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Whole Transcriptome Analysis of Hypertension Induced Cardiac Injury Using Deep Sequencing

Cellular Physiology and Biochemistry ◽

10.1159/000438659 ◽

2016 ◽

Vol 38 (2) ◽

pp. 670-682 ◽

Cited By ~ 4

Author(s):

Tao-Tao Li ◽

Xiao-Yan Li ◽

Li-Xin Jia ◽

Jing Zhang ◽

Wen-Mei Zhang ◽

...

Keyword(s):

Transcriptome Analysis ◽

Cell Activation ◽

Critical Role ◽

Cardiac Injury ◽

Interaction Network ◽

Receptor Interaction ◽

Rna Seq ◽

Cardiac Inflammation ◽

Molecular Events ◽

Focal Adhesion Protein

Background/Aims: Hypertension plays a critical role in the cardiac inflammation and injury. However, the mechanism of how hypertension causes the cardiac injury at a molecular level remains to be elucidated. Methods: RNA-Seq has been demonstrated to be an effective approach for transcriptome analysis, which is essential to reveal the molecular constituents of cells and tissues. In this study, we investigated the global molecular events associated with the mechanism of hypertension induced cardiac injury using RNA-Seq analysis. Results: Our results showed that totally 1,801 genes with different expression variations were identified after Ang II infusion at 1, 3 and 7 days. Go analysis showed that the top 5 high enrichment Go terms were response to stress, response to wounding, cellular component organization, cell activation and defense response. KEGG pathway analysis revealed the top 5 significantly overrepresented pathways were associated with ECM-receptor interaction, focal adhesion, protein digestion and absorption, phagosome and asthma. Moreover, protein-protein interaction network analysis indicated that ubiquitin C may play a key role in the processes of hypertension-induced cardiac injury. Conclusion: Our study provides a comprehensive understanding of the transcriptome events in hypertension-induced cardiac pathology.

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Quantitative effects of environmental variation on stomatal anatomy and gas exchange in a grass model

10.1101/2021.11.10.468085 ◽

2021 ◽

Author(s):

Tiago DG Nunes ◽

Magdalena W Slawinska ◽

Heike Lindner ◽

Michael T Raissig

Keyword(s):

Gas Exchange ◽

Anatomical Variation ◽

Brachypodium Distachyon ◽

Carbon Assimilation ◽

Light Response ◽

Gas Analysis ◽

Environmental Signals ◽

Grass Model ◽

Kinetics Of

Stomata are cellular pores on the leaf epidermis that allow plants to regulate carbon assimilation and water loss. Stomata integrate environmental signals to regulate pore apertures and optimize gas exchange to fluctuating conditions. Here, we quantified intraspecific plasticity of stomatal gas exchange and anatomy in response to seasonal variation in Brachypodium distachyon. Over the course of two years we (i) used infrared gas analysis to assess light response kinetics of 120 Bd21-3 wild-type individuals in an environmentally fluctuating greenhouse and (ii) microscopically determined the seasonal variability of stomatal anatomy in a subset of these plants. We observed systemic environmental effects on gas exchange measurements and remarkable intraspecific plasticity of stomatal anatomical traits. To reliably link anatomical variation to gas exchange, we adjusted anatomical gsmax calculations for grass stomatal morphology. We propose that systemic effects and variability in stomatal anatomy should be accounted for in long-term gas exchange studies.

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LED light gradient as a screening tool for light quality responses in model plant species

10.1101/2020.10.08.320002 ◽

2020 ◽

Author(s):

P. Lejeune ◽

A. Fratamico ◽

F. Bouché ◽

S. Huerga Fernández ◽

P. Tocquin ◽

...

Keyword(s):

Brachypodium Distachyon ◽

Production Costs ◽

Fluorescent Light ◽

Plant Responses ◽

Light Spectrum ◽

Crop Species ◽

Phenotypic Data ◽

Euphorbia Peplus ◽

Light Gradient ◽

Species Specific

AbstractCurrent developments in light-emitting diodes (LEDs) technologies have opened new perspectives for sustainable and highly efficient indoor cultivation. The introduction of LEDs not only allows a reduction in the production costs on a quantitative level, it also offers opportunities to manipulate and optimise qualitative traits. Indeed, while plants respond strongest to red and blue lights for photosynthesis, the whole light spectrum has an effect on plant shape, development, and chemical composition. In order to evaluate LEDs as an alternative to traditional lighting sources, the species-specific plant responses to distinct wavelengths need to be evaluated under controlled conditions. Here, we tested the possibility to use light composition gradients in combination with semi-automated phenotyping to rapidly explore the phenotypic responses of different species to variations in the light spectrum provided by LED sources. Plants of seven different species (Arabidopsis thaliana, Ocimum basilicum, Solanum lycopersicum, Brachypodium distachyon, Oryza sativa, Euphorbia peplus, Setaria viridis) were grown under standard white fluorescent light for 30 days, then transferred to a Red:Blue gradient for another 30 days and finally returned to white light. In all species, differences in terms of dimension, shape, and color were rapidly observed across the gradient and the overall response was widely species-dependent. The experiment yielded large amounts of imaging-based phenotypic data and we suggest simple data analysis methods to aggregate the results and facilitate comparisons between species. Similar experimental setups will help achieve rapid environmental optimization, screen new crop species and genotypes, or develop new gene discovery strategies.

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Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators

10.1101/680181 ◽

2019 ◽

Author(s):

Ru-pin Alicia Chi ◽

Tianyuan Wang ◽

Nyssa Adams ◽

San-pin Wu ◽

Steven L. Young ◽

...

Keyword(s):

Molecular Mechanisms ◽

Rna Seq ◽

Uterine Receptivity ◽

Normal Cycle ◽

Estrogen Response ◽

Molecular Events ◽

History Of ◽

And Function ◽

Genomic Regions ◽

Fertile Women

ABSTRACTContextPoor uterine receptivity is one major factor leading to pregnancy loss and infertility. Understanding the molecular events governing successful implantation is hence critical in combating infertility.ObjectiveTo define PGR-regulated molecular mechanisms and epithelial roles in receptivity.DesignRNA-seq and PGR-ChIP-seq were conducted in parallel to identify PGR-regulated pathways during the WOI in endometrium of fertile women.SettingEndometrial biopsies from the proliferative and mid-secretory phases were analyzed.Patients or Other ParticipantsParticipants were fertile, reproductive aged (18-37) women with normal cycle length; and without any history of dysmenorrhea, infertility, or irregular cycles. In total, 42 endometrial biopsies obtained from 42 women were analyzed in this study.InterventionsThere were no interventions during this study.Main Outcome MeasuresHere we measured the alterations in gene expression and PGR occupancy in the genome during the WOI, based on the hypothesis that PGR binds uterine chromatin cycle-dependently to regulate genes involved in uterine cell differentiation and function.Results653 genes were identified with regulated PGR binding and differential expression during the WOI. These were involved in regulating inflammatory response, xenobiotic metabolism, EMT, cell death, interleukin/STAT signaling, estrogen response, and MTORC1 response. Transcriptome of the epithelium identified 3,052 DEGs, of which 658 were uniquely regulated. Transcription factors IRF8 and MEF2C were found to be regulated in the epithelium during the WOI at the protein level, suggesting potentially important functions that are previously unrecognized.ConclusionPGR binds the genomic regions of genes regulating critical processes in uterine receptivity and function.PrécisUsing a combination of RNA-seq and PGR ChIP-seq, novel signaling pathways and epithelial regulators were identified in the endometrium of fertile women during the window of implantation.

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