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Special Issue "Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development"

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

Deadline for manuscript submissions: 29 February 2020.

Special Issue Editors

Dr. Maurizio Chiurazzi
E-Mail Website
Guest Editor
Consiglio Nazionale delle Ricerche, Institute of BioSciences and BioResourses, Rome, Italy
Interests: symbiotic nitrogen fixation; nitrogen use efficiency; nitrate transport; ammonium transport; plant transformation; root development; nodule organogenesis
Special Issues and Collections in MDPI journals
Dr. Vladimir Totev Valkov
E-Mail Website
Co-Guest Editor
Consiglio Nazionale delle Ricerche, Institute of Biosciences and Bioresources, Rome, Italy
Interests: nitrate transporters; nodule organogenesis; plastid gene expression; plastid transformation; plant–bacteria interactions

Special Issue Information

Dear Colleagues,

A comprehensive understanding of plant genomes with detailed and accurate analyses of associated gene expression is of crucial importance for both fundamental research and practical applications. Transcriptomics methodologies have developed considerably in the last decade, allowing analyses of expression in plants in response to environmental changes. This information is important for the investigation of the plethora of signaling pathways involved in the control of plant development and for the elucidation of the plant resilience capacity to fluctuating growth conditions. These studies are integrated with genetic approaches, leading to the identification of functional developmental modules. In this Special Issue, entitled “Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development”, research contributions on plant gene expression profiles in different environmental conditions, as well as the functional characterization of genes involved in plant development, will be highlighted, with a particular enphasis on the mechanisms of plant responses to nutrient availability changes.

Dr. Maurizio Chiurazzi
Dr. Vladimir Totev Valkov
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Plant development
  • Signaling
  • Gene expression
  • Nutrient availability.

Published Papers (4 papers)

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Research

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Open AccessArticle
Transgenerational Response to Nitrogen Deprivation in Arabidopsis thaliana
Int. J. Mol. Sci. 2019, 20(22), 5587; https://doi.org/10.3390/ijms20225587 - 08 Nov 2019
Abstract
Nitrogen (N) deficiency is one of the major stresses that crops are exposed to. It is plausible to suppose that a stress condition can induce a memory in plants that might prime the following generations. Here, an experimental setup that considered four successive [...] Read more.
Nitrogen (N) deficiency is one of the major stresses that crops are exposed to. It is plausible to suppose that a stress condition can induce a memory in plants that might prime the following generations. Here, an experimental setup that considered four successive generations of N-sufficient and N-limited Arabidopsis was used to evaluate the existence of a transgenerational memory. The results demonstrated that the ability to take up high amounts of nitrate is induced more quickly as a result of multigenerational stress exposure. This behavior was paralleled by changes in the expression of nitrate responsive genes. RNAseq analyses revealed the enduring modulation of genes in downstream generations, despite the lack of stress stimulus in these plants. The modulation of signaling and transcription factors, such as NIGTs, NFYA and CIPK23 might indicate that there is a complex network operating to maintain the expression of N-responsive genes, such as NRT2.1, NIA1 and NIR. This behavior indicates a rapid acclimation of plants to changes in N availability. Indeed, when fourth generation plants were exposed to N limitation, they showed a rapid induction of N-deficiency responses. This suggests the possible involvement of a transgenerational memory in Arabidopsis that allows plants to adapt efficiently to the environment and this gives an edge to the next generation that presumably will grow in similar stressful conditions. Full article
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Open AccessArticle
Nitrogen Starvation Differentially Influences Transcriptional and Uptake Rate Profiles in Roots of Two Maize Inbred Lines with Different NUE
Int. J. Mol. Sci. 2019, 20(19), 4856; https://doi.org/10.3390/ijms20194856 - 30 Sep 2019
Abstract
Nitrogen use efficiency (NUE) of crops is estimated to be less than 50%, with a strong impact on environment and economy. Genotype-dependent ability to cope with N shortage has been only partially explored in maize and, in this context, the comparison of molecular [...] Read more.
Nitrogen use efficiency (NUE) of crops is estimated to be less than 50%, with a strong impact on environment and economy. Genotype-dependent ability to cope with N shortage has been only partially explored in maize and, in this context, the comparison of molecular responses of lines with different NUE is of particular interest in order to dissect the key elements underlying NUE. Changes in root transcriptome and NH4+/NO3 uptake rates during growth (after 1 and 4 days) without N were studied in high (Lo5) and low (T250) NUE maize inbred lines. Results suggests that only a small set of transcripts were commonly modulated in both lines in response to N starvation. However, in both lines, transcripts linked to anthocyanin biosynthesis and lateral root formation were positively affected. On the contrary, those involved in root elongation were downregulated. The main differences between the two lines reside in the ability to modulate the transcripts involved in the transport, distribution and assimilation of mineral nutrients. With regard to N mineral forms, only the Lo5 line responded to N starvation by increasing the NH4+ fluxes as supported by the upregulation of a transcript putatively involved in its transport. Full article
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Open AccessArticle
Dynamic Changes in Metabolite Accumulation and the Transcriptome during Leaf Growth and Development in Eucommia ulmoides
Int. J. Mol. Sci. 2019, 20(16), 4030; https://doi.org/10.3390/ijms20164030 - 18 Aug 2019
Abstract
Eucommia ulmoides Oliver is widely distributed in China. This species has been used mainly in medicine due to the high concentration of chlorogenic acid (CGA), flavonoids, lignans, and other compounds in the leaves and barks. However, the categories of metabolites, dynamic changes in [...] Read more.
Eucommia ulmoides Oliver is widely distributed in China. This species has been used mainly in medicine due to the high concentration of chlorogenic acid (CGA), flavonoids, lignans, and other compounds in the leaves and barks. However, the categories of metabolites, dynamic changes in metabolite accumulation and overall molecular mechanisms involved in metabolite biosynthesis during E. ulmoides leaf growth and development remain unknown. Here, a total of 515 analytes, including 127 flavonoids, 46 organic acids, 44 amino acid derivatives, 9 phenolamides, and 16 vitamins, were identified from four E. ulmoides samples using ultraperformance liquid chromatography–mass spectrometry (UPLC-MS) (for widely targeted metabolites). The accumulation of most flavonoids peaked in growing leaves, followed by old leaves. UPLC-MS analysis indicated that CGA accumulation increased steadily to a high concentration during leaf growth and development, and rutin showed a high accumulation level in leaf buds and growing leaves. Based on single-molecule long-read sequencing technology, 69,020 transcripts and 2880 novel loci were identified in E. ulmoides. Expression analysis indicated that isoforms in the flavonoid biosynthetic pathway and flavonoid metabolic pathway were highly expressed in growing leaves and old leaves. Co-expression network analysis suggested a potential direct link between the flavonoid and phenylpropanoid biosynthetic pathways via the regulation of transcription factors, including MYB (v-myb avian myeloblastosis viral oncogene homolog) and bHLH (basic/helix-loop-helix). Our study predicts dynamic metabolic models during leaf growth and development and will support further molecular biological studies of metabolite biosynthesis in E. ulmoides. In addition, our results significantly improve the annotation of the E. ulmoides genome. Full article
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Review

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Open AccessReview
Impact of Nitrogen Nutrition on Cannabis sativa: An Update on the Current Knowledge and Future Prospects
Int. J. Mol. Sci. 2019, 20(22), 5803; https://doi.org/10.3390/ijms20225803 (registering DOI) - 18 Nov 2019
Abstract
Nitrogen (N) availability represents one of the most critical factors affecting cultivated crops. N is indeed a crucial macronutrient influencing major aspects, from plant development to productivity and final yield of lignocellulosic biomass, as well as content of bioactive molecules. N metabolism is [...] Read more.
Nitrogen (N) availability represents one of the most critical factors affecting cultivated crops. N is indeed a crucial macronutrient influencing major aspects, from plant development to productivity and final yield of lignocellulosic biomass, as well as content of bioactive molecules. N metabolism is fundamental as it is at the crossroad between primary and secondary metabolic pathways: Besides affecting the synthesis of fundamental macromolecules, such as nucleic acids and proteins, N is needed for other types of molecules intervening in the response to exogenous stresses, e.g. alkaloids and glucosinolates. By partaking in the synthesis of phenylalanine, N also directly impacts a central plant metabolic ‘hub’—the phenylpropanoid pathway—from which important classes of molecules are formed, notably monolignols, flavonoids and other types of polyphenols. In this review, an updated analysis is provided on the impact that N has on the multipurpose crop hemp (Cannabis sativa L.) due to its renewed interest as a multipurpose crop able to satisfy the needs of a bioeconomy. The hemp stalk provides both woody and cellulosic fibers used in construction and for biocomposites; different organs (leaves/flowers/roots) are sources of added-value secondary metabolites, namely cannabinoids, terpenes, flavonoids, and lignanamides. We survey the available literature data on the impact of N in hemp and highlight the importance of studying those genes responding to both N nutrition and abiotic stresses. Available hemp transcriptomic datasets obtained on plants subjected to salt and drought are here analyzed using Gene Ontology (GO) categories related to N metabolism. The ultimate goal is to shed light on interesting candidate genes that can be further studied in hemp varieties growing under different N feeding conditions and showing high biomass yield and secondary metabolite production, even under salinity and drought. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Transgenerational response to nitrogen deprivation in Arabidopsis thaliana

Author: Laura Zanin

Title: The Impact of Nitrogen Nutrition on Cannabis sativa: an update on the current knowledge and future prospects

Author: Gea Guerriero

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