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Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 20883

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Prof. Dr. Wilfried Rozhon

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Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
Interests: plant nutrition; orphan crops; analytical methods, including HPLC, UHPLC, GC, mass spectrometry, optical spectroscopy, electrophoresis and quantitative PCR; separation and analysis of chiral molecules; enzyme assays; inhibitors
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Dr. Sabine von Tucher

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Professorship of Crop Physiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 12, 85350 Freising, Germany
Interests: nutrient (use) efficiency (particularly P, S, N) in the plant–soil system; effectiveness of mineral and organic fertilizers as a source for the plant P, S and N demand; plant nutritional quality as affected by mineral nutrition; nutrient turnover in the environment
Special Issues, Collections and Topics in MDPI journals

Dr. Pecinka Ales

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The Czech Academy of Sciences, Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), 77900 Olomouc, Czech Republic
Interests: chromatin; epigenetics; genome stability; DNA damage repair; chromosomes; chromatin organization; SMC complexes; seed development; DNA methylation; transposons; epigenetic inhibitors; polyploidy; genome organization; Arabidopsis; barley

Special Issue Information

Dear Colleagues,

Inadequate plant nutrition is one of the major yield-limiting factors, and high agricultural productivity cannot be conceived of without a sufficient nutrient supply of crops. Minerals present in crop plants, particularly iron, potassium, and a number of micronutrients, are also crucial for human and livestock health. For instance, several hundred million people suffer from anemia due to lack of iron in their diet.

However, while the application of fertilizers enhances plant productivity and may positively affect nutritional value, overfertilization might reduce plant growth, cause accumulation of critical compounds like nitrate in vegetables, and have adverse effects on the environment, including contamination of surface and groundwater, evolution of the potent greenhouse gas nitrous oxide into the atmosphere, and algal bloom in lakes, rivers and the sea. In addition, there is an increasing shortage of some mineral resources, particularly phosphate. Thus, measures for need-based and resource-efficient fertilization are of utmost importance for the future.

To tackle these issues, a detailed understanding of the responses of plants to nutrients and nutrient deficiency at the physiological, metabolic, transcriptome, and epigenetic level is essential. While symptoms of malnutrition for specific elements have been known since the late 19th century, only in the last few decades have metabolic adaptations and the underlying regulation mechanisms been revealed. Importantly, in recent years, chromatin modifications in response to plant nutrition have also been studied in more detail.

Current topics of high significance include analysis of metabolic fluxes and relocalization of nutrients from senescent leaves to young tissues, and the regulation of these processes at the molecular level. Recent evidence suggests involvement of plant hormones in these regulatory processes, but detailed knowledge concerning signal transduction pathways involved remains scarce. Furthermore, the impact of minerals on primary and secondary plant metabolism, for instance phenolic compounds, pigments and alkaloids, and on redox homeostasis is of high relevance.

In many cases, essential nutrients, particularly transition metals, are present in the soil, but uptake by plants is impeded by environmental factors, such as the pH of the substrate. However, plants have evolved sophisticated strategies, for instance, production and exudation of chelating compounds, for the extraction of such elements from the growth substrate. Detailed knowledge regarding these processes will be important for the development of more efficient fertilization strategies.

Recent studies show that nutrient deficiency may cause massive changes in DNA methylation patterns, chromatin changes, and histone modifications. However, how these alterations impact on plant transcriptomes and potentially on transgenerational adaptations is so far poorly understood.

Original research articles, short communications, and reviews addressing the aforementioned or similar topics are considered attractive contributions for this Special Issue. For reviews, a brief proposal should be communicated prior to manuscript preparation to avoid overlap with other submissions.

Dr. Rozhon Wilfried
Dr. Sabine von Tucher
Dr. Pecinka Ales
Guest Editors

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

Plant nutrition
Primary and secondary metabolism
Chromatin modifications
Macro nutrients
Micro nutrients
Nitrogen
Phosphorous
Potassium
Sulfur
Magnesium
Calcium
Iron

Published Papers (7 papers)

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Editorial

Jump to: Research

4 pages, 527 KiB

Open AccessEditorial

Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications

by Fatema Binte Hafiz, Sabine von Tucher and Wilfried Rozhon

Int. J. Mol. Sci. 2022, 23(8), 4084; https://doi.org/10.3390/ijms23084084 - 07 Apr 2022

Cited by 1 | Viewed by 1689

Abstract

Plant growth and crop yield highly depend on the availability of all required nutrients, ideally in well-balanced ratios [...] Full article

(This article belongs to the Special Issue Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications)

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Research

Jump to: Editorial

27 pages, 27804 KiB

Open AccessArticle

Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice (Oryza sativa L.)

by Ting Liang, Zhengqing Yuan, Lu Fu, Menghan Zhu, Xiaoyun Luo, Wuwu Xu, Huanran Yuan, Renshan Zhu, Zhongli Hu and Xianting Wu

Int. J. Mol. Sci. 2021, 22(14), 7674; https://doi.org/10.3390/ijms22147674 - 18 Jul 2021

Cited by 13 | Viewed by 2868

Abstract

Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH₄NO₃ (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH₄NO₃ (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress. Full article

(This article belongs to the Special Issue Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications)

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20 pages, 2464 KiB

Open AccessArticle

Modulation of Phosphate Deficiency-Induced Metabolic Changes by Iron Availability in Arabidopsis thaliana

by Ranju Chutia, Sarah Scharfenberg, Steffen Neumann, Steffen Abel and Jörg Ziegler

Int. J. Mol. Sci. 2021, 22(14), 7609; https://doi.org/10.3390/ijms22147609 - 16 Jul 2021

Cited by 8 | Viewed by 2550

Abstract

Concurrent suboptimal supply of several nutrients requires the coordination of nutrient-specific transcriptional, phenotypic, and metabolic changes in plants in order to optimize growth and development in most agricultural and natural ecosystems. Phosphate (P_i) and iron (Fe) deficiency induce overlapping but mostly opposing transcriptional and root growth responses in Arabidopsis thaliana. On the metabolite level, P_i deficiency negatively modulates Fe deficiency-induced coumarin accumulation, which is controlled by Fe as well as P_i deficiency response regulators. Here, we report the impact of Fe availability on seedling growth under P_i limiting conditions and on P_i deficiency-induced accumulation of amino acids and organic acids, which play important roles in P_i use efficiency. Fe deficiency in P_i replete conditions hardly changed growth and metabolite profiles in roots and shoots of Arabidopsis thaliana, but partially rescued growth under conditions of P_i starvation and severely modulated P_i deficiency-induced metabolic adjustments. Analysis of T-DNA insertion lines revealed the concerted coordination of metabolic profiles by regulators of Fe (FIT, bHLH104, BRUTUS, PYE) as well as of P_i (SPX1, PHR1, PHL1, bHLH32) starvation responses. The results show the interdependency of P_i and Fe availability and the interplay between P_i and Fe starvation signaling on the generation of plant metabolite profiles. Full article

(This article belongs to the Special Issue Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications)

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20 pages, 2579 KiB

Open AccessArticle

Insights into the Role of Transcriptional Gene Silencing in Response to Herbicide-Treatments in Arabidopsis thaliana

by Catarine Markus, Ales Pecinka and Aldo Merotto, Jr.

Int. J. Mol. Sci. 2021, 22(7), 3314; https://doi.org/10.3390/ijms22073314 - 24 Mar 2021

Cited by 12 | Viewed by 2765

Abstract

Herbicide resistance is broadly recognized as the adaptive evolution of weed populations to the intense selection pressure imposed by the herbicide applications. Here, we tested whether transcriptional gene silencing (TGS) and RNA-directed DNA Methylation (RdDM) pathways modulate resistance to commonly applied herbicides. Using Arabidopsis thaliana wild-type plants exposed to sublethal doses of glyphosate, imazethapyr, and 2,4-D, we found a partial loss of TGS and increased susceptibility to herbicides in six out of 11 tested TGS/RdDM mutants. Mutation in REPRESSOR OF SILENCING 1 (ROS1), that plays an important role in DNA demethylation, leading to strongly increased susceptibility to all applied herbicides, and imazethapyr in particular. Transcriptomic analysis of the imazethapyr-treated wild type and ros1 plants revealed a relation of the herbicide upregulated genes to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis, and epigenetic processes. Hypersensitivity to imazethapyr of the flavonoid biosynthesis component TRANSPARENT TESTA 4 (TT4) mutant plants strongly suggests that ROS1-dependent accumulation of flavonoids is an important mechanism for herbicide stress response in A. thaliana. In summary, our study shows that herbicide treatment affects transcriptional gene silencing pathways and that misregulation of these pathways makes Arabidopsis plants more sensitive to herbicide treatment. Full article

(This article belongs to the Special Issue Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications)

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13 pages, 5756 KiB

Open AccessArticle

Heterologous Expression of Nitrate Assimilation Related-Protein DsNAR2.1/NRT3.1 Affects Uptake of Nitrate and Ammonium in Nitrogen-Starved Arabidopsis

by Hongping Ma, Junchao Zhao, Shuang Feng, Kun Qiao, Shufang Gong, Jingang Wang and Aimin Zhou

Int. J. Mol. Sci. 2020, 21(11), 4027; https://doi.org/10.3390/ijms21114027 - 04 Jun 2020

Cited by 11 | Viewed by 2422

Abstract

Nitrogen (N) is an essential macronutrient for plant growth. Plants absorb and utilize N mainly in the form of nitrate (NO₃⁻) or ammonium (NH₄⁺). In this study, the nitrate transporter DsNRT3.1 (also known as the nitrate assimilation-related protein DsNAR2.1) was characterized from Dianthus spiculifolius. A quantitative PCR (qPCR) analysis showed that the DsNRT3.1 expression was induced by NO₃⁻. Under N-starvation conditions, the transformed Arabidopsis seedlings expressing DsNRT3.1 had longer roots and a greater fresh weight than the wild type. Subcellular localization showed that DsNRT3.1 was mainly localized to the plasma membrane in Arabidopsis root hair cells. Non-invasive micro-test (NMT) monitoring showed that the root hairs of N-starved transformed Arabidopsis seedlings had a stronger NO₃⁻ and NH₄⁺ influx than the wild-type seedlings, using with NO₃⁻ or NH₄⁺ as the sole N source; contrastingly, transformed seedlings only had a stronger NO₃⁻ influx when NO₃⁻ and NH₄⁺ were present simultaneously. In addition, the qPCR analysis showed that the expression of AtNRT2 genes (AtNRT2.1–2.6), and particularly of AtNRT2.5, in the transformed Arabidopsis differed from that in the wild type. Overall, our results suggest that the heterologous expression of DsNRT3.1 affects seedlings’ growth by enhancing the NO₃⁻ and NH₄⁺ uptake in N-starved Arabidopsis. This may be related to the differential expression of AtNRT2 genes. Full article

(This article belongs to the Special Issue Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications)

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21 pages, 4274 KiB

Open AccessArticle

The Role of Gibberellins in Regulation of Nitrogen Uptake and Physiological Traits in Maize Responding to Nitrogen Availability

by Yubin Wang, Qingqing Yao, Yushi Zhang, Yuexia Zhang, Jiapeng Xing, Benzhou Yang, Guohua Mi, Zhaohu Li and Mingcai Zhang

Int. J. Mol. Sci. 2020, 21(5), 1824; https://doi.org/10.3390/ijms21051824 - 06 Mar 2020

Cited by 26 | Viewed by 3737

Abstract

Modified gibberellin (GA) signaling leads to semi-dwarfism with low nitrogen (N) use efficiency (NUE) in crops. An understanding of GA-mediated N uptake is essential for the development of crops with improved NUE. The function of GA in modulating N uptake capacity and nitrate (NO₃⁻) transporters (NRTs) was analyzed in the GA synthesis-deficient mutant zmga3ox grown under low (LN) and sufficient (SN) N conditions. LN significantly suppressed the production of GA₁, GA_3, and GA₄, and the zmga3ox plants showed more sensitivity in shoots as well as LN stress. Moreover, the higher anthocyanin accumulation and the decrease of chlorophyll content were also recorded. The net NO₃⁻ fluxes and ¹⁵N content were decreased in zmga3ox plants under both LN and SN conditions. Exogenous GA₃ could restore the NO₃⁻ uptake in zmga3ox plants, but uniconazole repressed NO₃⁻ uptake. Moreover, the transcript levels of ZmNRT2.1/2.2 were downregulated in zmga3ox plants, while the GA₃ application enhanced the expression level. Furthermore, the RNA-seq analyses identified several transcription factors that are involved in the GA-mediated transcriptional operation of NRTs related genes. These findings revealed that GAs influenced N uptake involved in the transcriptional regulation of NRTs and physiological responses in maize responding to nitrogen supply. Full article

(This article belongs to the Special Issue Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications)

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14 pages, 5703 KiB

Open AccessArticle

Overexpression of OsPIN2 Regulates Root Growth and Formation in Response to Phosphate Deficiency in Rice

by Huwei Sun, Xiaoli Guo, Fugui Xu, Daxia Wu, Xuhong Zhang, Manman Lou, Feifei Luo, Guohua Xu and Yali Zhang

Int. J. Mol. Sci. 2019, 20(20), 5144; https://doi.org/10.3390/ijms20205144 - 17 Oct 2019

Cited by 28 | Viewed by 3117

Abstract

The response of root architecture to phosphate (P) deficiency is critical in plant growth and development. Auxin is a key regulator of plant root growth in response to P deficiency, but the underlying mechanisms are unclear. In this study, phenotypic and genetic analyses were undertaken to explore the role of OsPIN2, an auxin efflux transporter, in regulating the growth and development of rice roots under normal nutrition condition (control) and low-phosphate condition (LP). Higher expression of OsPIN2 was observed in rice plants under LP compared to the control. Meanwhile, the auxin levels of roots were increased under LP relative to control condition in wild-type (WT) plants. Compared to WT plants, two overexpression (OE) lines had higher auxin levels in the roots under control and LP. LP led to increased seminal roots (SRs) length and the root hairs (RHs) density, but decreased lateral roots (LRs) density in WT plants. However, overexpression of OsPIN2 caused a loss of sensitivity in the root response to P deficiency. The OE lines had a shorter SR length, lower LR density, and greater RH density than WT plants under control. However, the LR and RH densities in the OE lines were similar to those in WT plants under LP. Compared to WT plants, overexpression of OsPIN2 had a shorter root length through decreased root cell elongation under control and LP. Surprisingly, overexpression of OsPIN2 might increase auxin distribution in epidermis of root, resulting in greater RH formation but less LR development in OE plants than in WT plants in the control condition but levels similar of these under LP. These results suggest that higher OsPIN2 expression regulates rice root growth and development maybe by changing auxin distribution in roots under LP condition. Full article

(This article belongs to the Special Issue Plant Nutrition: Physiological and Metabolic Responses, Molecular Mechanisms and Chromatin Modifications)

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