Identification, Evolution, Expression, and Docking Studies of Fatty Acid Desaturase Genes in Wheat (Triticum aestivum L.)

Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture.

Section: Discussionsupporting

confidence: 86%

Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families

Puccio,

Ingraffia,

Giambalvo

et al. 2023

“…Genes associated with the JA biosynthesis pathway, FAD8 and SSI2, were induced only in the CTN+ vs CTN-comparison, and showed a repressed expression pattern comparing INN+ vs CTN+. Fatty acid desaturases (FADs) introduce a double bond in the acyl chain of fatty acids, resulting in unsaturated fatty acids participating in the first steps of JA synthesis and playing essential roles in response to biotic and abiotic stresses (Hajiahmadi et al, 2020). Previous work in Arabidopsis showed that fad3-2 fad7-2 fad8 plants showed reduced defense response to root rot caused by the root pathogen Pythium mastophorum, while wild-type plants were not affected by this fungus (Reymond and Farmer, 1998).…”

Section: Modulation Of Plant Hormonal Signaling By Nitrogen Fertiliza...mentioning

confidence: 99%

Dual RNA-seq of maize and H. seropedicae ZAE94 association, in different doses of nitrate, reveals novel insights into Plant-PGPB-environment relationship

Rosman,

Urquiaga,

Thiebaut

et al. 2024

The interactions between plants, beneficial bacteria and their environment are profoundly shaped by various environmental factors, including light, temperature, water availability, and soil quality. Despite efforts to elucidate the molecular mechanisms involved in the association between plants and beneficial bacteria, like Plant Growth-Promoting Bacteria (PGPB), with many studies focusing on the transcriptional reprogramming in the plant, there is no report on the modulation of genetic controls from both plant and associated bacteria standpoints, in response to environment. The main goal of this study was to investigate the relationship between plant-bacteria-environment signaling, using as a model maize plants inoculated with H. seropedicae ZAE94 and cultivated with different doses of N (0.3 and 3 mM). For this purpose, we performed rRNA-depleted RNA-seq to determine the global gene expression of both maize roots and associated H. seropedicae ZAE94. Our results revealed a differential modulation of maize nitrogen metabolism, phytohormone and cell wall responses when associated with H. seropedicae ZAE94 at different N concentrations. In parallel, a modulation of the bacterial metabolism could be observed, by regulating genes involved in transport, secretion system, cell mobility, oxidoreductases, and chemotaxis, when bacteria were associated with maize roots and cultivated at different doses of N. The molecular and phenotypic data of maize plantlets suggested that different doses of N fertilization differentially regulated the beneficial effects of bacterial inoculation, as higher doses (3 mM) favored shoot elongation and lower doses (0.3 mM) favored increase in plant biomass. Our results provide a valuable integrated overview of differentially expressed genes in both maize and associated H. seropedicae ZAE94 in response to different N availability, revealing new insights into pathways involved in grass-PGPB associations.

“…Additionally, plant aconitases are also known to mediate other physiological processes like oxidative stress, lipid metabolism, glyoxylate cycle, sucrose metabolism, and the regulation of cell death (Wang et al, 2016). In previous studies, it is stated that FADS enzymes contain conserved histidine-rich sequences in their active sites as is present in verified divalent iron enzymes and catalyzes the desaturation of fatty acids in various forms which help in the regulation of fatty acid composition and maintenance of membrane fluidity under abiotic and biotic stress conditions (Zhao et al, 2019;Hajiahmadi et al, 2020). The PAPs enzymes require binuclear chromophoric metal ions (Fe/Zn or Fe/Mn) for their activity and are known to play vital roles in the maintenance of Pi acquisition and utilization, cellulose and carbon metabolism, fixation of nitrogen, reactive oxygen species (ROS) metabolism, response to nutrients, and other environmental stresses and pathogen defences (Olczak et al, 2003).…”

mentioning

confidence: 99%

A systematic in silico report on iron and zinc proteome of Zea mays

Sharma,

Verma

2023

Zea mays is an essential staple food crop across the globe. Maize contains macro and micronutrients but is limited in essential mineral micronutrients such as Fe and Zn. Worldwide, serious health concerns have risen due to the deficiencies of essential nutrients in human diets, which rigorously jeopardizes economic development. In the present study, the systematic in silico approach has been used to predict Fe and Zn binding proteins from the whole proteome of maize. A total of 356 and 546 putative proteins have been predicted, which contain sequence and structural motifs for Fe and Zn ions, respectively. Furthermore, the functional annotation of these predicted proteins, based on their domains, subcellular localization, gene ontology, and literature support, showed their roles in distinct cellular and biological processes, such as metabolism, gene expression and regulation, transport, stress response, protein folding, and proteolysis. The versatile roles of these shortlisted putative Fe and Zn binding proteins of maize could be used to manipulate many facets of maize physiology. Moreover, in the future, the predicted Fe and Zn binding proteins may act as relevant, novel, and economical markers for various crop improvement programs.