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      The transcriptome of zinc deficient maize roots and its relationship to DNA methylation loss

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          Abstract

          Background

          Zinc (Zn) is an essential micronutrient of all organisms. Deficiency of zinc causes disturbance in crucial plant functions, as a high number of enzymes, including transcription factors, depend on zinc for proper performance. The plant responses to zinc deficiency are associated with increased high affinity Zn uptake and translocation, as well as efficient usage of the remaining zinc, but have not been characterized in molecular detail in maize.

          Results

          The high affinity transporter genes ZmZIP3,4,5,7 and 8 and nicotianamine synthases, primarily ZmNAS5, were identified as primary up-regulated in maize roots upon prolonged Zn deficiency. In addition to down-regulation of genes encoding enzymes involved in pathways regulating reactive oxygen species and cell wall-related genes, a massive up-regulation of the sucrose efflux channel genes SWEET13a,c was identified, despite that in –Zn sugar is known to accumulate in shoots. In addition, enzymes involved in DNA maintenance methylation tended to be repressed, which coincided with massively reduced DNA methylation in Zn-deficient roots. Reduced representation bisulfate sequencing, which revealed base-specific methylation patterns in ~ 14% of the maize genome, identified a major methylation loss in -Zn, mostly in transposable elements. However, hypermethylated genome regions in –Zn were also identified, especially in both symmetrical cytosine contexts. Differential methylation was partially associated with differentially expressed genes, their promoters, or transposons close to regulated genes. However, hypomethylation was associated with about equal number of up- or down-regulated genes, questioning a simple mechanistic relationship to gene expression.

          Conclusions

          The transcriptome of Zn-deficient roots identified genes and pathways to cope with the deficiency and a major down-regulation of reactive oxygen metabolism. Interestingly, a nutrient-specific loss of DNA methylation, partially related to gene expression in a context-specific manner, may play a role in long-term stress adaptation.

          Electronic supplementary material

          The online version of this article (10.1186/s12870-018-1603-z) contains supplementary material, which is available to authorized users.

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          Most cited references39

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          Zinc in plants.

          Zinc (Zn) is an essential component of thousands of proteins in plants, although it is toxic in excess. In this review, the dominant fluxes of Zn in the soil-root-shoot continuum are described, including Zn inputs to soils, the plant availability of soluble Zn(2+) at the root surface, and plant uptake and accumulation of Zn. Knowledge of these fluxes can inform agronomic and genetic strategies to address the widespread problem of Zn-limited crop growth. Substantial within-species genetic variation in Zn composition is being used to alleviate human dietary Zn deficiencies through biofortification. Intriguingly, a meta-analysis of data from an extensive literature survey indicates that a small proportion of the genetic variation in shoot Zn concentration can be attributed to evolutionary processes whose effects manifest above the family level. Remarkable insights into the evolutionary potential of plants to respond to elevated soil Zn have recently been made through detailed anatomical, physiological, chemical, genetic and molecular characterizations of the brassicaceous Zn hyperaccumulators Thlaspi caerulescens and Arabidopsis halleri.
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            Biogenesis, turnover, and mode of action of plant microRNAs.

            MicroRNAs (miRNAs) are small RNAs that control gene expression through silencing of target mRNAs. Mature miRNAs are processed from primary miRNA transcripts by the endonuclease activity of the DICER-LIKE1 (DCL1) protein complex. Mechanisms exist that allow the DCL1 complex to precisely excise the miRNA from its precursor. Our understanding of miRNA biogenesis, particularly its intersection with transcription and other aspects of RNA metabolism such as splicing, is still evolving. Mature miRNAs are incorporated into an ARGONAUTE (AGO) effector complex competent for target gene silencing but are also subjected to turnover through a degradation mechanism that is beginning to be understood. The mechanisms of miRNA target silencing in plants are no longer limited to AGO-catalyzed slicing, and the contribution of translational inhibition is increasingly appreciated. Here, we review the mechanisms underlying the biogenesis, turnover, and activities of plant miRNAs.
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              Neue Methode zur Bestimmung des Stickstoffs in organischen Körpern

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                Author and article information

                Contributors
                svenja.mager@uni-hohenheim.de
                Brigitte_Schoenberger@uni-hohenheim.de
                +4971145922344 , u.ludewig@uni-hohenheim.de
                Journal
                BMC Plant Biol
                BMC Plant Biol
                BMC Plant Biology
                BioMed Central (London )
                1471-2229
                27 December 2018
                27 December 2018
                2018
                : 18
                : 372
                Affiliations
                ISNI 0000 0001 2290 1502, GRID grid.9464.f, Institute of Crop Science, Nutritional Crop Physiology, , University of Hohenheim, ; Fruwirthstr. 20, 70593 Stuttgart, Germany
                Author information
                http://orcid.org/0000-0001-5456-1055
                Article
                1603
                10.1186/s12870-018-1603-z
                6307195
                30587136
                b53a798d-fa39-40b1-99f9-df59b5d5803e
                © The Author(s). 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 16 August 2018
                : 12 December 2018
                Funding
                Funded by: Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg (DE)
                Award ID: 1
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2018

                Plant science & Botany
                zinc,dna methylation,maize,gene expression,genome stability,transposable elements

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