Zinc finger transcription factor ZAT family genes confer multi-tolerances in Gossypium hirsutum L.

AbstractZAT (Zinc Finger of Arabidopsis thaliana) proteins are composed of a plant-specific transcription factor family, which play an important role in plant growth, development, and stress resistance. To study the potential function of ZAT family in cotton, the whole genome identification, expression, and structure analysis of ZAT gene family were carried out. In this study, our analysis revealed the presence of 115, 56, 59, and 115 ZAT genes in Gossypium hirsutum, G. raimondii, G. arboreum and G. barbadense, respectively. According to the number of domains and phylogenetic characteristics, we divided ZAT genes of four Gossypium species into 4 different clades, and further divided them into 11 subfamilies. The results of collinearity analysis showed that segmental duplication was the main method to amplify the cotton ZAT genes family. Analysis of cis-elements of promoters indicated that most GhZAT genes contained cis-elements related to plant hormones and abiotic stress. According to heatmap analysis, the expression patterns of GhZAT genes under different stresses indicated that GhZAT genes were significantly involved in the response to cold, heat, salt, and PEG stress, possibly through different mechanisms. Among the highly expressed genes, we cloned a G. hirsutum gene GhZAT67. Through virus-induced gene silencing (VIGS), we found that its expression level decreased significantly after being silenced. Under alkaline treatment, the wilting degree of silenced plants was even greater than the wild type, which proved that GhZAT67 gene was involved in the response to alkaline stress.

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EIL2 Transcription Factor and Glutathione Synthetase Are Required for Defense of Tobacco Against Tobacco Blue Mold

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-19-0399 ◽

2006 ◽

Vol 19 (4) ◽

pp. 399-406 ◽

Cited By ~ 16

Author(s):

Orlando Borrás-Hidalgo ◽

Bart P. H. J. Thomma ◽

Cyrelys Collazo ◽

Osmany Chacón ◽

Carlos J. Borroto ◽

...

Keyword(s):

Transcription Factor ◽

Lipid Transfer Protein ◽

Expression Patterns ◽

Differentially Expressed ◽

Glutathione Synthetase ◽

Lipid Transfer ◽

Virus Induced Gene Silencing ◽

Incompatible Interaction ◽

Blue Mold ◽

Mold Resistance

In order to identify tobacco (Nicotiana megalosiphon) genes involved in broad-spectrum resistance to tobacco blue mold (Peronospora hyoscyami f. sp. tabacina), suppression subtractive hybridization was used to generate cDNA from transcripts that are differentially expressed during an incompatible interaction. After differential screening by membrane-based hybridization, clones corresponding to 182 differentially expressed genes were selected, sequenced, and analyzed. The cDNA collection comprised a broad repertoire of genes associated with various processes. Northern blot analysis of a subset of these genes confirmed the differential expression patterns between the compatible and incompatible interaction. Subsequent virus-induced gene silencing (VIGS) of four genes that were found to be differentially induced was pursued. While VIGS of a lipid transfer protein gene or a glutamate decarboxylase gene in Nicotiana megalosiphon did not affect blue mold resistance, silencing of an EIL2 transcription factor gene and a glutathione synthetase gene was found to compromise the resistance of Nicotiana megalosiphon to P. hyoscyami f. sp. tabacina. Potentially, these genes can be used to engineer resistance in blue mold-susceptible tobacco cultivars.

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Genome-Wide Analysis of the YABBY Transcription Factor Family in Pineapple and Functional Identification of AcYABBY4 Involvement in Salt Stress

International Journal of Molecular Sciences ◽

10.3390/ijms20235863 ◽

2019 ◽

Vol 20 (23) ◽

pp. 5863 ◽

Cited By ~ 2

Author(s):

Zeyun Li ◽

Gang Li ◽

Mingxing Cai ◽

Samaranayaka V.G.N. Priyadarshani ◽

Mohammad Aslam ◽

...

Keyword(s):

Transcription Factor ◽

Salt Stress ◽

Protein Structure ◽

Zinc Finger ◽

Structure Prediction ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Regulatory Role ◽

Short Root ◽

Finger Protein

The plant-specific transcription factor gene family, YABBY, belongs to the subfamily of zinc finger protein superfamily and plays an essential regulatory role in lateral organ development. In this study, nine YABBY genes were identified in the pineapple genome. Seven of them were located on seven different chromosomes and the remaining two were located on scaffold 1235. Through protein structure prediction and protein multiple sequence alignment, we found that AcYABBY3, AcYABBY5 and AcYABBY7 lack a C2 structure in their N-terminal C2C2 zinc finger protein structure. Analysis of the cis-acting element indicated that all the seven pineapple YABBY genes contain multiple MYB and MYC elements. Further, the expression patterns analysis using the RNA-seq data of different pineapple tissues indicated that different AcYABBYs are preferentially expressed in various tissues. RT-qPCR showed that the expression of AcYABBY2, AcYABBY3, AcYABBY6 and AcYABBY7 were highly sensitive to abiotic stresses. Subcellular localization in pineapple protoplasts, tobacco leaves and Arabidopsis roots showed that all the seven pineapple YABBY proteins were nucleus localized. Overexpression of AcYABBY4 in Arabidopsis resulted in short root under NaCl treatment, indicating a negative regulatory role of AcYABBY4 in plant resistance to salt stress. This study provides valuable information for the classification of pineapple AcYABBY genes and established a basis for further research on the functions of AcYABBY proteins in plant development and environmental stress response.

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Using Transcriptome to Discover a Novel Melatonin-Induced Sodic Alkaline Stress Resistant Pathway in Solanum lycopersicum L.

Plant and Cell Physiology ◽

10.1093/pcp/pcz126 ◽

2019 ◽

Vol 60 (9) ◽

pp. 2051-2064 ◽

Cited By ~ 21

Author(s):

Yanyan Yan ◽

Xin Jing ◽

Huimeng Tang ◽

Xiaotong Li ◽

Biao Gong ◽

...

Keyword(s):

Stress Tolerance ◽

Stress Responses ◽

Transcriptional Control ◽

Alkaline Treatment ◽

Transcriptional Factors ◽

Alkaline Stress ◽

Virus Induced Gene Silencing ◽

Downstream Signaling ◽

Ph Buffering ◽

Solanum Lycopersicum L

Abstract Melatonin plays important roles in multiple stress responses. However, the downstream signaling pathway and molecular mechanism are unclear until now. Here, we not only revealed the transcriptional control of melatonin-induced sodic alkaline stress tolerance, but also described a screen for key downstream transcriptional factors of melatonin through transcriptome analysis. The melatonin-induced transcriptional network of hormone, transcriptional factors and functional genes has been established under both control and stress conditions. Among these, six candidates of transcriptional factors have been identified via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Using the virus-induced gene silencing approach, we confirmed that DREB1α and IAA3 were key downstream transcriptional factors of melatonin-induced sodic alkaline stress tolerance at the genetic level. The transcriptions of DREB1α and IAA3 could be activated by melatonin or sodic alkaline treatment. Interestingly, we found that DREB1α could directly upregulate the expression of IAA3 by binding to its promoters. Moreover, several physiological processes of Na+ detoxification, dehydration resistance, high pH buffering and reactive oxygen species scavenging were confirmed to depend or partly depend on DREB1α and IAA3 pathway in melatonin-induced stress tolerance. Taken together, this study suggested that DREB1α and IAA3 are positive resistant modulators, and provided a direct link among melatonin, DREB1α and IAA3 in the sodic alkaline stress tolerance activating in tomato plants.

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Enhancer analysis of the Drosophila zinc finger transcription factor Earmuff by gene targeting

Hereditas ◽

10.1186/s41065-021-00209-6 ◽

2021 ◽

Vol 158 (1) ◽

Author(s):

Kirsten Hildebrandt ◽

Sabrina Kübel ◽

Marie Minet ◽

Nora Fürst ◽

Christine Klöppel ◽

...

Keyword(s):

Transcription Factor ◽

Gene Targeting ◽

Zinc Finger ◽

Neural Progenitor Cells ◽

Expression Patterns ◽

Brain Structures ◽

Systematic Analysis ◽

Major Function ◽

Stem Cell Maintenance ◽

The Brain

Abstract Background Many transcription factors are involved in the formation of the brain during the development of Drosophila melanogaster. The transcription factor Earmuff (Erm), a member of the forebrain embryonic zinc finger family (Fezf), is one of these important factors for brain development. One major function of Earmuff is the regulation of proliferation within type II neuroblast lineages in the brain; here, Earmuff is expressed in intermediate neural progenitor cells (INPs) and balances neuronal differentiation versus stem cell maintenance. Erm expression during development is regulated by several enhancers. Results In this work we show a functional analysis of erm and some of its enhancers. We generated a new erm mutant allele by gene targeting and reintegrated Gal4 to make an erm enhancer trap strain that could also be used on an erm mutant background. The deletion of three of the previously analysed enhancers showing the most prominent expression patterns of erm by gene targeting resulted in specific temporal and spatial defects in defined brain structures. These defects were already known but here could be assigned to specific enhancer regions. Conclusion This analysis is to our knowledge the first systematic analysis of several large enhancer deletions of a Drosophila gene by gene targeting and will enable deeper analysis of erm enhancer functions in the future.

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Genome-Wide Study of the GATL Gene Family in Gossypium hirsutum L. Reveals that GhGATL Genes Act on Pectin Synthesis to Regulate Plant Growth and Fiber Elongation

Genes ◽

10.3390/genes11010064 ◽

2020 ◽

Vol 11 (1) ◽

pp. 64

Author(s):

Lei Zheng ◽

Huanhuan Wu ◽

Ghulam Qanmber ◽

Faiza Ali ◽

Lingling Wang ◽

...

Keyword(s):

Plant Growth ◽

Gossypium Hirsutum ◽

Positive Selection ◽

Gene Family ◽

Selection Pressure ◽

Expression Patterns ◽

Control Plant ◽

Segmental Duplications ◽

Fiber Elongation ◽

Virus Induced Gene Silencing

Pectin is a major polysaccharide component that promotes plant growth and fiber elongation in cotton. In previous studies, the galacturonosyltransferase-like (GATL) gene family has been shown to be involved in pectin synthesis. However, few studies have been performed on cotton GATL genes. Here, a total of 33, 17, and 16 GATL genes were respectively identified in Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum. In multiple plant species, phylogenetic analysis divided GATL genes into five groups named GATL-a to GATL-e, and the number of groups was found to gradually change over evolution. Whole genome duplication (WGD) and segmental duplication played a significant role in the expansion of the GATL gene family in G. hirsutum. Selection pressure analyses revealed that GATL-a and GATL-b groups underwent a great positive selection pressure during evolution. Moreover, the expression patterns revealed that most of highly expressed GhGATL genes belong to GATL-a and GATL-b groups, which have more segmental duplications and larger positive selection value, suggesting that these genes may play an important role in the evolution of cotton plants. We overexpressed GhGATL2, GhGATL9, GhGATL12, and GhGATL15 in Arabidopsis and silenced the GhGATL15 gene in cotton through a virus induced gene silencing assay (VIGS). The transgenic and VIGS lines showed significant differences in stem diameter, epidermal hair length, stamen length, seed size, and fiber length than the control plant. In addition, the pectin content test proved that the pectin was significantly increased in the transgenic lines and reduced in VIGS plants, demonstrating that GhGATL genes have similar functions and act on the pectin synthesis to regulate plant growth and fiber elongation. In summary, we performed a comprehensive analysis of GhGATL genes in G. hirsutum including evolution, structure and function, in order to better understand GhGATL genes in cotton for further studies.

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Identification and Analysis of GhEXO Gene Family Indicated That GhEXO7_At Promotes Plant Growth and Development Through Brassinosteroid Signaling in Cotton (Gossypium hirsutum L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.719889 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shengdong Li ◽

Zhao Liu ◽

Guoquan Chen ◽

Ghulam Qanmber ◽

Lili Lu ◽

...

Keyword(s):

Plant Growth ◽

Gossypium Hirsutum ◽

Gene Family ◽

Growth And Development ◽

Expression Patterns ◽

Ectopic Expression ◽

Virus Induced Gene Silencing ◽

Plant Growth And Development ◽

Altered Expression ◽

Protein Motifs

Brassinosteroids (BRs), an efficient plant endogenous hormone, significantly promotes plant nutrient growth adapting to biological and abiotic adversities. BRs mainly promote plant cell elongation by regulating gene expression patterns. EXORDIUM (EXO) genes have been characterized as the indicators of BR response genes. Cotton, an ancient crop, is of great economic value and its fibers can be made into all kinds of fabrics. However, EXO gene family genes have not been full identified in cotton. 175 EXO genes were identified in nine plant species, of which 39 GhEXO genes in Gossypium hirsutum in our study. A phylogenetic analysis grouped all of the proteins encoded by the EXO genes into five major clades. Sequence identification of conserved amino acid residues among monocotyledonous and dicotyledonous species showed a high level of conservation across the N and C terminal regions. Only 25% the GhEXO genes contain introns besides conserved gene structure and protein motifs distribution. The 39 GhEXO genes were unevenly distributed on the 18 At and Dt sub-genome chromosomes. Most of the GhEXO genes were derived from gene duplication events, while only three genes showed evidence of tandem duplication. Homologous locus relationships showed that 15 GhEXO genes are located on collinear blocks and that all orthologous/paralogous gene pairs had Ka > Ks values, indicating purifying selection pressure. The GhEXO genes showed ubiquitous expression in all eight tested cotton tissues and following exposure to three phytohormones, IAA, GA, and BL. Furthermore, GhEXO7_At was mainly expressed in response to BL treatment, and was predominantly expressed in the fibers. GhEXO7_At was found to be a plasma membrane protein, and its ectopic expression in Arabidopsis mediated BR-regulated plant growth and development with altered expression of DWF4, CPD, KCS1, and EXP5. Additionally, the functions of GhEXO7_At were confirmed by virus-induced gene silencing (VIGS) in cotton. This study will provide important genetic resources for future cotton breeding programs.

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A zinc-finger fusion protein refines Gal4-defined neural circuits

10.1101/228718 ◽

2017 ◽

Author(s):

Shamprasad Varija Raghu ◽

Farhan Mohammad ◽

Chua Jia Yi ◽

Claudia S. Barros ◽

Joanne Lam ◽

...

Keyword(s):

Transcription Factor ◽

Dna Binding ◽

Fusion Protein ◽

Zinc Finger ◽

Neural Circuits ◽

Expression Patterns ◽

Genetic Fidelity ◽

Dna Binding Specificity ◽

Expression Control ◽

Gal4 Expression

AbstractThe analysis of behavior requires that the underlying neuronal circuits are identified and genetically isolated. In several major model species—most notably Drosophila, neurogeneticists identify and isolate neural circuits with a binary heterologous expression-control system: Gal4–UASG. One limitation of Gal4–UASG is that expression patterns are often too broad to map circuits precisely. To help refine the range of Gal4 lines, we developed an intersectional genetic AND operator. Interoperable with Gal4, the new system’s key component is a fusion protein in which the DNA-binding domain of Gal4 has been replaced with a zinc finger domain with a different DNA-binding specificity. In combination with its cognate binding site (UASZ) the zinc-finger-replaced Gal4 (‘Zal1’) was functional as a standalone transcription factor. Zal1 transgenes also refined Gal4 expression ranges when combined with UASGZ, a hybrid upstream activation sequence. In this way, combining Gal4 and Zal1 drivers captured restricted cell sets compared with single drivers and improved genetic fidelity. This intersectional genetic AND operation presumably derives from the action of a heterodimeric transcription factor: Gal4-Zal1. Configurations of Zal1–UASZ and Zal1-Gal4-UASGZ are versatile tools for defining, refining, and manipulating targeted neural expression patterns with precision.

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