Functions of the ERF transcription factor family in plants

Botany ◽  
2008 ◽  
Vol 86 (9) ◽  
pp. 969-977 ◽  
Author(s):  
Zhao-Shi Xu ◽  
Ming Chen ◽  
Lian-Cheng Li ◽  
You-Zhi Ma
Keyword(s):  
Stress Responses ◽  
Phylogenetic Relationships ◽  
Biological Functions ◽  
Transcription Factor Family ◽  
Conserved Motifs ◽  
Over Expression ◽  
Wide Range ◽  
Erf Family ◽  
Gene Structures ◽  
Disease Resistances

Ethylene responsive factors (ERFs) play vital regulatory roles in a variety of developmental processes and stress responses in plants. In this study, ERF family genes in a wide range of plant species were classified into 8 clusters and 14 subclusters on the basis of phylogenetic relationships, gene structures, conserved motifs, and biological functions. ERF genes, especially those in Clusters II and VII, can be used as candidates to improve crop-plant resistance because their over-expression enhances multiple disease resistances and improves tolerances to drought, salt, and freezing in transgenic plants. The comprehensive analysis of phylogenetic relationships, conserved motifs, and physiological functions is useful in elucidating the biological roles of ERF family genes in signal transduction, gene regulation, and defense response under stress environments.

scholarly journals Genome-Wide Identification of Aluminum-Activated Malate Transporter (ALMT) Gene Family in Rubber Trees (Hevea brasiliensis) Highlights Their Involvement in Aluminum Detoxification

Forests ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 142
Author(s):  
Xiaowei Ma ◽  
Feng An ◽  
Lifeng Wang ◽  
Dong Guo ◽  
Guishui Xie ◽  
...  
Keyword(s):  
Hevea Brasiliensis ◽  
Phylogenetic Relationships ◽  
Expression Patterns ◽  
Rubber Tree ◽  
Pcr Analysis ◽  
Cis Elements ◽  
Conserved Motifs ◽  
Gene Structures ◽  
Different Tissues ◽  
Malate Transporter

The rubber tree (Hevea brasiliensis) is a widely cultivated crop in tropical acidic soil that is tolerant to high concentration of aluminum and the aluminum-activated malate transporter (ALMT) plays an important role in plant aluminum detoxification. However, the effects of ALMT on rubber tree aluminum tolerance, growth performance, and latex production are unclear. In this study, 17 HbALMT genes were identified from the genome of rubber trees. The physiological and biochemical characteristics, phylogenetic relationships, gene structures, conserved motifs, cis-elements of promoter, and expression patterns of the identified HbALMT genes were studied. Phylogenetic relationships indicated that these genes were divided into four clusters and genes in the same cluster have similar gene structures and conserved motifs. The promoters of HbALMT genes contain many cis-elements associated with biotic stress and abiotic stress. Quantitative real-time PCR analysis revealed HbALMTs showed various expression patterns in different tissues, indicating the functional diversity of HbALMT genes in different tissues of rubber trees. Transcriptome analysis and qRT-PCR assay showed that most of the HbALMT genes responded to aluminum stress, and among the 17 HbALMTs, HbALMT1, HbALMT2, HbALMT13, and HbALMT15 displayed higher expression levels in roots after two or five days of Al treatments, indicating their potential involvement in aluminum detoxification. Taken together, this study laid a foundation for further understanding the molecular evolution of the ALMT genes and their involvement in rubber tree aluminum adaption.

scholarly journals Genome-Wide Identification of the B-BOX Genes that Respond to Multiple Ripening Related Signals in Sweet Cherry Fruit

2021 ◽  
Vol 22 (4) ◽  
pp. 1622
Author(s):  
Yanyan Wang ◽  
Zefeng Zhai ◽  
Yueting Sun ◽  
Chen Feng ◽  
Xiang Peng ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Stress Responses ◽  
Fruit Development ◽  
Sweet Cherry ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Light Induction ◽  
Promoter Regions ◽  
Genome Database ◽  
Gene Structures

B-BOX proteins are zinc finger transcription factors that play important roles in plant growth, development, and abiotic stress responses. In this study, we identified 15 PavBBX genes in the genome database of sweet cherry. We systematically analyzed the gene structures, clustering characteristics, and expression patterns of these genes during fruit development and in response to light and various hormones. The PavBBX genes were divided into five subgroups. The promoter regions of the PavBBX genes contain cis-acting elements related to plant development, hormones, and stress. qRT-PCR revealed five upregulated and eight downregulated PavBBX genes during fruit development. In addition, PavBBX6, PavBBX9, and PavBBX11 were upregulated in response to light induction. We also found that ABA, BR, and GA3 contents significantly increased in response to light induction. Furthermore, the expression of several PavBBX genes was highly correlated with the expression of anthocyanin biosynthesis genes, light-responsive genes, and genes that function in multiple hormone signaling pathways. Some PavBBX genes were strongly induced by ABA, GA, and BR treatment. Notably, PavBBX6 and PavBBX9 responded to all three hormones. Taken together, BBX proteins likely play major roles in regulating anthocyanin biosynthesis in sweet cherry fruit by integrating light, ABA, GA, and BR signaling pathways.

scholarly journals Antimicrobial Nodule-Specific Cysteine-Rich Peptides Induce Membrane Depolarization-Associated Changes in the Transcriptome of Sinorhizobium meliloti

2013 ◽  
Vol 79 (21) ◽  
pp. 6737-6746 ◽  
Author(s):  
Hilda Tiricz ◽  
Attila Szűcs ◽  
Attila Farkas ◽  
Bernadett Pap ◽  
Rui M. Lima ◽  
...  
Keyword(s):  
Stress Responses ◽  
Sinorhizobium Meliloti ◽  
Antimicrobial Agents ◽  
Cellular Functions ◽  
Gram Positive ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Peptide Family ◽  
Wide Range ◽  
Natural Target

ABSTRACTLeguminous plants establish symbiosis with nitrogen-fixing alpha- and betaproteobacteria, collectively called rhizobia, which provide combined nitrogen to support plant growth. Members of the inverted repeat-lacking clade of legumes impose terminal differentiation on their endosymbiotic bacterium partners with the help of the nodule-specific cysteine-rich (NCR) peptide family composed of close to 600 members. Among the few tested NCR peptides, cationic ones had antirhizobial activity measured by reduction or elimination of the CFU and uptake of the membrane-impermeable dye propidium iodide. Here, the antimicrobial spectrum of two of these peptides, NCR247 and NCR335, was investigated, and their effect on the transcriptome of the natural targetSinorhizobium melilotiwas characterized. Both peptides were able to kill quickly a wide range of Gram-negative and Gram-positive bacteria; however, their spectra were only partially overlapping, and differences were found also in their efficacy on given strains, indicating that the actions of NCR247 and NCR335 might be similar though not identical. Treatment ofS. meliloticultures with either peptide resulted in a quick downregulation of genes involved in basic cellular functions, such as transcription-translation and energy production, as well as upregulation of genes involved in stress and oxidative stress responses and membrane transport. Similar changes provoked mainly in Gram-positive bacteria by antimicrobial agents were coupled with the destruction of membrane potential, indicating that it might also be a common step in the bactericidal actions of NCR247 and NCR335.

scholarly journals Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination

2009 ◽  
Vol 106 (17) ◽  
pp. 7251-7256 ◽  
Author(s):  
Atsushi Fukushima ◽  
Miyako Kusano ◽  
Norihito Nakamichi ◽  
Makoto Kobayashi ◽  
Naomi Hayashi ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Stress Responses ◽  
Clock Genes ◽  
Higher Plants ◽  
Tricarboxylic Acid Cycle ◽  
Integrated Analysis ◽  
Response Regulators ◽  
Triple Mutant ◽  
Mitochondrial Functions ◽  
Wide Range

In higher plants, the circadian clock controls a wide range of cellular processes such as photosynthesis and stress responses. Understanding metabolic changes in arrhythmic plants and determining output-related function of clock genes would help in elucidating circadian-clock mechanisms underlying plant growth and development. In this work, we investigated physiological relevance of PSEUDO-RESPONSE REGULATORS (PRR 9, 7, and 5) in Arabidopsis thaliana by transcriptomic and metabolomic analyses. Metabolite profiling using gas chromatography–time-of-flight mass spectrometry demonstrated well-differentiated metabolite phenotypes of seven mutants, including two arrhythmic plants with similar morphology, a PRR 9, 7, and 5 triple mutant and a CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1)-overexpressor line. Despite different light and time conditions, the triple mutant exhibited a dramatic increase in intermediates in the tricarboxylic acid cycle. This suggests that proteins PRR 9, 7, and 5 are involved in maintaining mitochondrial homeostasis. Integrated analysis of transcriptomics and metabolomics revealed that PRR 9, 7, and 5 negatively regulate the biosynthetic pathways of chlorophyll, carotenoid and abscisic acid, and α-tocopherol, highlighting them as additional outputs of pseudo-response regulators. These findings indicated that mitochondrial functions are coupled with the circadian system in plants.

scholarly journals WRKY Proteins: Signaling and Regulation of Expression during Abiotic Stress Responses

2015 ◽  
Vol 2015 ◽  
pp. 1-17 ◽  
Author(s):  
Aditya Banerjee ◽  
Aryadeep Roychoudhury
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Biotic Stress ◽  
Abiotic Stresses ◽  
Abiotic Stress Tolerance ◽  
Plant Signaling ◽  
Biological Functions ◽  
Abiotic And Biotic Stress ◽  
Regulation Of Expression ◽  
Wrky Proteins

WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of theWRKYgenes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research.

scholarly journals Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

2020 ◽  
Author(s):  
R. H. Sammour ◽  
M. A. Karam ◽  
Y. S. Morsi ◽  
R. M. Ali
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships ◽  
Fixation Index ◽  
Distribution Area ◽  
Enzyme Analysis ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

scholarly journals The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2169
Author(s):  
Hailian Zhou ◽  
Jiaying Li ◽  
Xueyuan Liu ◽  
Xiaoshuang Wei ◽  
Ziwei He ◽  
...  
Keyword(s):  
Plant Development ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Brown Planthopper ◽  
Protein Structures ◽  
Secondary Growth ◽  
Primary Cell Wall ◽  
Biological Functions ◽  
Group I

Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. β-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.

scholarly journals Hexokinase and glucokinases are essential for fitness and virulence in the pathogenic yeastCandida albicans

2018 ◽  
Author(s):  
Romain Laurian ◽  
Karine Dementhon ◽  
Bastien Doumèche ◽  
Alexandre Soulard ◽  
Thierry Noel ◽  
...  
Keyword(s):  
Stress Responses ◽  
Galleria Mellonella ◽  
Glucose Repression ◽  
Metabolic Adaptation ◽  
Metabolic Flexibility ◽  
Pathogenic Yeast ◽  
Regulatory Pathways ◽  
Metabolic Role ◽  
Wide Range ◽  
Hexose Phosphorylation

AbstractMetabolic flexibility promotes infection and commensal colonization by the opportunistic pathogenCandida albicans.Yeast cell survival depends upon assimilation of fermentable and non-fermentable locally available carbon sources. Physiologically relevant sugars like glucose and fructose are present at low level in host niches. However, because glucose is the preferred substrate for energy and biosynthesis of structural components, its efficient metabolization is fundamental for the metabolic adaptation of the pathogen. We explored and characterized theC. albicanshexose kinase system composed of one hexokinase (CaHxk2) and two glucokinases (CaGlk1 and CaGlk4). Using a set of mutant strains, we found that hexose phosphorylation is mostly assured by CaHxk2, which sustains growth on hexoses. Our data on hexokinase and glucokinase expression point out an absence of cross regulation mechanisms at the transcription level and different regulatory pathways. In the presence of glucose, CaHxk2 migrates in the nucleus and contributes to the glucose repression signaling pathway. In addition, CaHxk2 participates to oxidative, osmotic and cell wall stress responses, while glucokinases are overexpressed under hypoxia. Hexose phosphorylation is a key step necessary for filamentation, that is affected in the hexokinase mutant. Virulence of this mutant is clearly impacted in theGalleria mellonellaand macrophage models. Filamentation, glucose phosphorylation and stress response defects of the hexokinase mutant prevent host killing byC. albicans.By contributing to metabolic flexibility, stress answer response and morphogenesis, hexose kinase enzymes play an essential role in the virulence ofC. albicans.Author summaryThe pathogenic yeastC. albicansis both a powerful commensal and pathogen of humans that can infect wide range of organs and body sites. To grow in its host and establish an infection, the pathogen must assimilate carbon from these heterogenous environments.C. albicansregulates central carbon metabolism in a niche-specific manner, activating alternatively gluconeogenesis, glyoxylate cycle and the glycolytic metabolism. For yeast and other microorganisms, glucose is the preferred carbon and energy source and its accurate detection and metabolism is essential. However, the glycolytic hexose kinase system has not been investigated yet inC. albicans.In this report, we showed that hexokinase and glucokinases contribute to the fitness and virulence ofC. albicans.We revealed the main metabolic role of the hexokinase CaHxk2 which impacts on growth, glucose signalling, morphological transition and virulence. However, glucokinases contribute to the anoxic response and their implication in regulation processes is suggested.

scholarly journals Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

2019 ◽  
Author(s):  
Yongbin Wang ◽  
Zhenfeng Jiang ◽  
Zhenxiang Li ◽  
Yuanling Zhao ◽  
Weiwei Tan ◽  
...  
Keyword(s):  
Glycine Max ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Biological Functions ◽  
Conserved Domain ◽  
Genome Wide ◽  
Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

scholarly journals Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species

2021 ◽  
Vol 17 (2) ◽  
pp. e1008767
Author(s):  
Zutan Li ◽  
Hangjin Jiang ◽  
Lingpeng Kong ◽  
Yuanyuan Chen ◽  
Kun Lang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Prediction Accuracy ◽  
Cross Validation ◽  
Biological Processes ◽  
Biological Functions ◽  
Learning Framework ◽  
Wide Range ◽  
Genomic Scale ◽  
Downstream Gene Expression ◽  
Fold Cross Validation

N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA’s biological functions. However, the existing experimental techniques for detecting 6mA sites are cost-ineffective, which implies the great need of developing new computational methods for this problem. In this paper, we developed, without requiring any prior knowledge of 6mA and manually crafted sequence features, a deep learning framework named Deep6mA to identify DNA 6mA sites, and its performance is superior to other DNA 6mA prediction tools. Specifically, the 5-fold cross-validation on a benchmark dataset of rice gives the sensitivity and specificity of Deep6mA as 92.96% and 95.06%, respectively, and the overall prediction accuracy is 94%. Importantly, we find that the sequences with 6mA sites share similar patterns across different species. The model trained with rice data predicts well the 6mA sites of other three species: Arabidopsis thaliana, Fragaria vesca and Rosa chinensis with a prediction accuracy over 90%. In addition, we find that (1) 6mA tends to occur at GAGG motifs, which means the sequence near the 6mA site may be conservative; (2) 6mA is enriched in the TATA box of the promoter, which may be the main source of its regulating downstream gene expression.

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