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Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development 2.0

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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 (20 November 2021) | Viewed by 16177

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Special Issue Editors

Dr. Maurizio Chiurazzi

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Guest Editor

Consiglio Nazionale delle Ricerche, Institute of BioSciences and BioResourses, Rome, Italy
Interests: symbiotic N-fixation; nutrient transporters; signaling pathways
Special Issues, Collections and Topics in MDPI journals

Dr. Vladimir Totev Valkov

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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

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Keywords

Plant development
Signaling
Gene expression
Nutrient availability

Published Papers (7 papers)

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Research

19 pages, 4126 KiB

Open AccessArticle

Comparative Transcriptome Analysis Revealed the Key Genes Regulating Ascorbic Acid Synthesis in Actinidia

by Xiaoying Liu, Xiaodong Xie, Caihong Zhong and Dawei Li

Int. J. Mol. Sci. 2021, 22(23), 12894; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222312894 - 29 Nov 2021

Cited by 6 | Viewed by 2073

Abstract

Actinidia (kiwifruit) is known as ‘the king of vitamin C’ due to its rich ascorbic acid (AsA) concentration, which makes it an important model for studying the regulation of AsA metabolism. Herein, transcriptomic analysis was employed to identify candidate genes that regulate AsA synthesis in Actinidia species with 100-fold variations in fruit AsA content (A. latifolia and A. rufa). Approximately 1.16 billion high-quality reads were generated, and an average of 66.68% of the data was uniquely aligned against the reference genome. AsA-associated DEGs that predominately respond to abiotic signals, and secondary metabolic pathways were identified. The key candidate genes, for instance, GDP-L-galactose phosphorylase-3 (GGP3), were explored according to integrated analysis of the weighted gene co-expression network and L-galactose pathway. Transgenic kiwifruit plants were generated, and the leaves of GGP3 (OE-GGP3) overexpressing lines had AsA contents 2.0- to 6.4-fold higher than those of the wild type. Transcriptomic analysis of transgenic kiwifruit lines was further implemented to identify 20 potential downstream target genes and understand GGP3-regulated cellular processes. As a result, two transcription factors (AcESE3 and AcMYBR) were selected to carry out yeast two-hybrid and BiFC assays, which verified that there were obvious AcESE3–AcMYBR and AcESE3–AcGGP3 protein–protein interactions. This study provides insight into the mechanism of AsA synthesis and provides candidate factors and genes involved in AsA accumulation in kiwifruit. Full article

(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development 2.0)

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18 pages, 4057 KiB

Open AccessArticle

Nitrate Regulates Maize Root Transcriptome through Nitric Oxide Dependent and Independent Mechanisms

by Laura Ravazzolo, Sara Trevisan, Silvia Iori, Cristian Forestan, Mario Malagoli and Silvia Quaggiotti

Int. J. Mol. Sci. 2021, 22(17), 9527; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22179527 - 02 Sep 2021

Cited by 1 | Viewed by 1987

Abstract

Maize root responds to nitrate by modulating its development through the coordinated action of many interacting players. Nitric oxide is produced in primary root early after the nitrate provision, thus inducing root elongation. In this study, RNA sequencing was applied to discover the main molecular signatures distinguishing the response of maize root to nitrate according to their dependency on, or independency of, nitric oxide, thus discriminating the signaling pathways regulated by nitrate through nitric oxide from those regulated by nitrate itself of by further downstream factors. A set of subsequent detailed functional annotation tools (Gene Ontology enrichment, MapMan, KEGG reconstruction pathway, transcription factors detection) were used to gain further information and the lateral root density was measured both in the presence of nitrate and in the presence of nitrate plus cPTIO, a specific NO scavenger, and compared to that observed for N-depleted roots. Our results led us to identify six clusters of transcripts according to their responsiveness to nitric oxide and to their regulation by nitrate provision. In general, shared and specific features for the six clusters were identified, allowing us to determine the overall root response to nitrate according to its dependency on nitric oxide. Full article

(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development 2.0)

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16 pages, 2708 KiB

Open AccessArticle

Transcriptomic Characterization of Nitrate-Enhanced Stevioside Glycoside Synthesis in Stevia (Stevia rebaudiana) Bertoni

by Yuming Sun, Ting Zhang, Xiaoyang Xu, Yongheng Yang, Haiying Tong, Luis Alejandro Jose Mur and Haiyan Yuan

Int. J. Mol. Sci. 2021, 22(16), 8549; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22168549 - 09 Aug 2021

Cited by 7 | Viewed by 2543

Abstract

Nitrogen forms (nitrate (NO₃⁻) or ammonium (NH₄⁺)) are vital to plant growth and metabolism. In stevia (Stevia rebaudiana), it is important to assess whether nitrogen forms can influence the synthesis of the high-value terpene metabolites-steviol glycosides (SGs), together with the underlying mechanisms. Field and pot experiments were performed where stevia plants were fertilized with either NO₃⁻ or NH₄⁺ nutrition to the same level of nitrogen. Physiological measurements suggested that nitrogen forms had no significant impact on biomass and the total nitrogen content of stevia leaves, but NO₃⁻-enhanced leaf SGs contents. Transcriptomic analysis identified 397 genes that were differentially expressed (DEGs) between NO₃⁻ and NH₄⁺ treatments. Assessment of the DEGs highlighted the responses in secondary metabolism, particularly in terpenoid metabolism, to nitrogen forms. Further examinations of the expression patterns of SGs synthesis-related genes and potential transcription factors suggested that GGPPS and CPS genes, as well as the WRKY and MYB transcription factors, could be driving N form-regulated SG synthesis. We concluded that NO₃⁻, rather than NH₄⁺, can promote leaf SG synthesis via the NO₃⁻-MYB/WRKY-GGPPS/CPS module. Our study suggests that insights into the molecular mechanism of how SG synthesis can be affected by nitrogen forms. Full article

(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development 2.0)

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19 pages, 8018 KiB

Open AccessArticle

The Lotus japonicus AFB6 Gene Is Involved in the Auxin Dependent Root Developmental Program

by Alessandra Rogato, Vladimir Totev Valkov, Marcin Nadzieja, Jens Stougaard and Maurizio Chiurazzi

Int. J. Mol. Sci. 2021, 22(16), 8495; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22168495 - 06 Aug 2021

Cited by 2 | Viewed by 1726

Abstract

Auxin is essential for root development, and its regulatory action is exerted at different steps from perception of the hormone up to transcriptional regulation of target genes. In legume plants there is an overlap between the developmental programs governing lateral root and N₂-fixing nodule organogenesis, the latter induced as the result of the symbiotic interaction with rhizobia. Here we report the characterization of a member of the L. japonicus TIR1/AFB auxin receptor family, LjAFB6. A preferential expression of the LjAFB6 gene in the aerial portion of L. japonicus plants was observed. Significant regulation of the expression was not observed during the symbiotic interaction with Mesorhizobium loti and the nodule organogenesis process. In roots, the LjAFB6 expression was induced in response to nitrate supply and was mainly localized in the meristematic regions of both primary and lateral roots. The phenotypic analyses conducted on two independent null mutants indicated a specialized role in the control of primary and lateral root elongation processes in response to auxin, whereas no involvement in the nodulation process was found. We also report the involvement of LjAFB6 in the hypocotyl elongation process and in the control of the expression profile of an auxin-responsive gene. Full article

(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development 2.0)

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21 pages, 81435 KiB

Open AccessArticle

Structure, Distribution, Chemical Composition, and Gene Expression Pattern of Glandular Trichomes on the Leaves of Rhus potaninii Maxim

by Qin Lu, Nawaz Haider Bashir, Hai-Xia Wu, Weiwei Wang, Jinwen Zhang, Yongzhong Cui and Hang Chen

Int. J. Mol. Sci. 2021, 22(14), 7312; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147312 - 07 Jul 2021

Cited by 1 | Viewed by 2250

Abstract

Rhus potaninii Maxim is an economically and medicinally important tree species in China. It produces galls (induced by aphids) with a high abundance of tannins. Here, we discuss the histology, cellular structures and their distribution, and the macromolecular components of secretive glandular trichomes on the leaves of R. potaninii. A variation in the density of glandular trichomes and tomenta was found between the adaxial and abaxial sides of a leaf in different regions and stages of the leaf. The glandular trichomes on R. potaninii trees comprise a stalk with no cellular structure and a head with 8–15 cells. Based on staining, we found that the secretion of glandular trichomes has many polysaccharides, phenolic compounds, and acidic lipids but very few neutral lipids. The dense glandular trichomes provide mechanical protection for young tissues; additionally, their secretion protects the young tissues from pathogens by a special chemical component. According to transcriptome analysis, we found enhanced biosynthetic and metabolism pathways of glycan, lipids, toxic amino acids, and phenylpropanoids. This shows a similar tendency to the staining. The numbers of differentially expressed genes were large or small; the averaged range of upregulated genes was greater than that of the downregulated genes in most subpathways. Some selectively expressed genes were found in glandular trichomes, responsible for the chitinase activity and pathogenesis-related proteins, which all have antibacterial activity and serve for plant defense. To our knowledge, this is the first study showing the components of the secretion from glandular trichomes on the leaf surface of R. potaninii. Full article

(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development 2.0)

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19 pages, 29876 KiB

Open AccessArticle

Transcriptome and Metabolomic Analyses Reveal Regulatory Networks Controlling Maize Stomatal Development in Response to Blue Light

by Tiedong Liu and Xiwen Zhang

Int. J. Mol. Sci. 2021, 22(10), 5393; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22105393 - 20 May 2021

Cited by 9 | Viewed by 2424

Abstract

(1) Background: Blue light is important for the formation of maize stomata, but the signal network remains unclear. (2) Methods: We replaced red light with blue light in an experiment and provided a complementary regulatory network for the stomatal development of maize by using transcriptome and metabolomics analysis. (3) Results: Exposure to blue light led to 1296 differentially expressed genes and 419 differential metabolites. Transcriptome comparisons and correlation signaling network analysis detected 55 genes, and identified 6 genes that work in the regulation of the HY5 module and MAPK cascade, that interact with PTI1, COI1, MPK2, and MPK3, in response to the substitution of blue light in environmental adaptation and signaling transduction pathways. Metabolomics analysis showed that two genes involved in carotenoid biosynthesis and starch and sucrose metabolism participate in stomatal development. Their signaling sites located on the PHI1 and MPK2 sites of the MAPK cascade respond to blue light signaling. (4) Conclusions: Blue light remarkably changed the transcriptional signal transduction and metabolism of metabolites, and eight obtained genes worked in the HY5 module and MAPK cascade. Full article

(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development 2.0)

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30 pages, 6896 KiB

Open AccessArticle

Molecular and Histologic Adaptation of Horned Gall Induced by the Aphid Schlechtendalia chinensis (Pemphigidae)

by Qin Lu, Xiaoming Chen, Zixiang Yang, Nawaz Haider Bashir, Juan Liu, Yongzhong Cui, Shuxiao Shao, Ming-Shun Chen and Hang Chen

Int. J. Mol. Sci. 2021, 22(10), 5166; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22105166 - 13 May 2021

Cited by 3 | Viewed by 1822

Abstract

Chinese galls are the result of hyperplasia in host plants induced by aphids. The metabolism and gene expression of these galls are modified to accommodate the aphids. Here, we highlight the molecular and histologic features of horned galls according to transcriptome and anatomical structures. In primary pathways, genes were found to be unevenly shifted and selectively expressed in the galls and leaves near the galls (LNG). Pathways for amino acid synthesis and degradation were also unevenly shifted, favoring enhanced accumulation of essential amino acids in galls for aphids. Although galls enhanced the biosynthesis of glucose, which is directly available to aphids, glucose content in the gall tissues was lower due to the feeding of aphids. Pathways of gall growth were up-regulated to provide enough space for aphids. In addition, the horned gall has specialized branched schizogenous ducts and expanded xylem in the stalk, which provide a broader feeding surface for aphids and improve the efficiency of transportation and nutrient exchange. Notably, the gene expression in the LNG showed a similar pattern to that of the galls, but on a smaller scale. We suppose the aphids manipulate galls to their advantage, and galls lessen competition by functioning as a medium between the aphids and their host plants. Full article

(This article belongs to the Special Issue Transcriptomic Basis and Nutrient Dependent Signaling Pathways in Plant Development 2.0)

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