scholarly journals Characterization of the AP2/ERF Transcription Factor Family and Expression Profiling of DREB Subfamily under Cold and Osmotic Stresses in Ammopiptanthus nanus

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 455 ◽  
Author(s):  
Shilin Cao ◽  
Ying Wang ◽  
Xuting Li ◽  
Fei Gao ◽  
Jinchao Feng ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Expression Profiling ◽  
Segmental Duplications ◽  
Promoter Regions ◽  
Cold Response ◽  
Cis Acting ◽  
Ammopiptanthus Nanus ◽  
Erf Family ◽  
Responsive Element

APETALA2/ethylene-responsive factor (AP2/ERF) is one of the largest transcription factor (TF) families in plants, which play important roles in regulating plant growth, development, and response to environmental stresses. Ammopiptanthus nanus, an unusual evergreen broad-leaved shrub in the arid region in the northern temperate zone, demonstrates a strong tolerance to low temperature and drought stresses, and AP2/ERF transcription factors may contribute to the stress tolerance of A. nanus. In the current study, 174 AP2/ERF family members were identified from the A. nanus genome, and they were divided into five subfamilies, including 92 ERF members, 55 dehydration-responsive element binding (DREB) members, 24 AP2 members, 2 RAV members, and 1 Soloist member. Compared with the other leguminous plants, A. nanus has more members of the DREB subfamily and the B1 group of the ERF subfamily, and gene expansion in the AP2/ERF family is primarily driven by tandem and segmental duplications. Promoter analysis showed that many stress-related cis-acting elements existed in promoter regions of the DREB genes, implying that MYB, ICE1, and WRKY transcription factors regulate the expression of DREB genes in A. nanus. Expression profiling revealed that the majority of DREB members were responsive to osmotic and cold stresses, and several DREB genes such as EVM0023336.1 and EVM0013392.1 were highly induced by cold stress, which may play important roles in cold response in A. nanus. This study provided important data for understanding the evolution and functions of AP2/ERF and DREB transcription factors in A. nanus.

scholarly journals Transcriptional Regulation of the Gene Encoding an Alcohol Dehydrogenase in the Archaeon Sulfolobus solfataricus Involves Multiple Factors and Control Elements

2003 ◽  
Vol 185 (13) ◽  
pp. 3926-3934 ◽  
Author(s):  
Gabriella Fiorentino ◽  
Raffaele Cannio ◽  
Mosè Rossi ◽  
Simonetta Bartolucci
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Alcohol Dehydrogenase ◽  
Molecular Mechanisms ◽  
Environmental Changes ◽  
Sulfolobus Solfataricus ◽  
Regulatory Sequences ◽  
Mobility Shift ◽  
Tata Element ◽  
Responsive Element

ABSTRACT A transcriptionally active region has been identified in the 5′ flanking region of the alcohol dehydrogenase gene of the crenarchaeon Sulfolobus solfataricus through the evaluation of the activity of putative transcriptional regulators and the role of the region upstream of the gene under specific metabolic circumstances. Electrophoretic mobility shift assays with crude extracts revealed protein complexes that most likely contain TATA box-associated factors. When the TATA element was deleted from the region, binding sites for both DNA binding proteins, such as the small chromatin structure-modeling Sso7d and Sso10b (Alba), and transcription factors, such as the repressor Lrs14, were revealed. To understand the molecular mechanisms underlying the substrate-induced expression of the adh gene, the promoter was analyzed for the presence of cis-acting elements recognized by specific transcription factors upon exposure of the cell to benzaldehyde. Progressive dissection of the identified promoter region restricted the analysis to a minimal responsive element (PAL) located immediately upstream of the transcription factor B-responsive element-TATA element, resembling typical bacterial regulatory sequences. A benzaldehyde-activated transcription factor (Bald) that specifically binds to the PAL cis-acting element was also identified. This protein was purified from heparin-fractionated extracts of benzaldehyde-induced cells and was shown to have a molecular mass of ∼16 kDa. The correlation between S. solfataricus adh gene activation and benzaldehyde-inducible occupation of a specific DNA sequence in its promoter suggests that a molecular signaling mechanism is responsible for the switch of the aromatic aldehyde metabolism as a response to environmental changes.

Association of SMAD3/4, COUP-Tf, HNF4α, C/EBPα, GATA2 and STAT5 to the Hamp1 Promoter

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3837-3837
Author(s):  
Pauline Lee ◽  
Jaroslav Truksa ◽  
Ernest Beutler
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Nuclear Extract ◽  
Proximal Region ◽  
Proximal Promoter ◽  
Bzip Transcription Factor ◽  
Mobility Shift ◽  
Nuclear Extracts ◽  
Genes Encoding ◽  
Responsive Element

Abstract There are two regions of the murine Hamp1 promoter that have been shown to be critical for Hamp1 expression. The 260 bp proximal region and the distal −1.6 to −1.8 Kb regions appear to be required for responsiveness to IL-6, BMPs and iron. Analyses of 160 bp proximal promoter for consensus transcription factor motifs by MatInspector identified a STAT5 site at the location identified previously by Wrighting et al., Blood 2006, as a functional STAT3 site and by Courselaud et al., J Biol Chem 2002, as a C/EBPα site. Although a SMAD responsive site was not predicted in this region, we (in press), and Verga-Falzacappa et al., J Mol Med 2008, have demonstrated that there is a functional BMP responsive element (GGCGCC) in this region. A probe encompassing the putative BMP-RE1, STAT, C/EBPα, and AP1 motifs were used in electrophoretic mobility shift assays (EMSA). We found that the addition of cold competitor DNA corresponding to STAT3, C/EBPα and AP1 consensus motifs did not block the binding of transcription factors from liver nuclear extracts to the BMP-RE1/STAT/C/EBPα/AP1 probe. In contrast, the addition of cold competitor DNA corresponding the SMAD3/4 or STAT5 completely blocked essentially all binding of liver nuclear transcription factors to the BMP-RE1/STAT/C/EBPα/AP1 probe. Analyses of the −161 to −260 bp proximal promoter for consensus transcription factor motifs identified a GATA2 binding site and a SMAD responsive site (TGTCTGCCC). Two long probes encompassing the to −161 to −260 bp region were used in EMSAs. Binding of liver nuclear extracts to a probe encompassing the GATA motif was blocked by the addition of a GATA consensus DNA. Similarly, binding to a long probe encompassing the SMAD responsive site was blocked by the addition of a SMAD3/4 consensus DNA. Analyses of the 1.6 to 1.7 Kb region of the distal murine Hamp1 promoter identified several transcription factor motifs: bZIP transcription factor that acts on nuclear genes encoding mitochondrial proteins, COUP-Tf/HNF4α, and MEL1 (MDS1/EVI1-like gene1) to be both in human and mouse Hamp genes. Although a SMAD responsive site was not identified in this region, we have demonstrated that there is a functional BMP responsive element (GGCGCC) in this region. Using EMSA with probes corresponding to the −1.6 to −1.7 bp region of the hepcidin promoter, we examined the binding of transcription factors from liver nuclear extracts derived from mice. Binding of liver nuclear extract to a probe corresponding to the BMP-RE2, bZIP, HNF4α, COUP motifs was blocked by cold competitor probes corresponding to SMAD3/4, HNF4α, COUP-Tf, and Stat5. Whereas competitor probes to Smad3/4 and HNF4α competed for the binding of specific bands to the radiolabelled probe, total binding was blocked with cold competitor probes to the consensus COUP-Tf and Stat5 motifs. Supershift analyses using antibodies to HNF4α, COUP, SMAD4 demonstrated the binding of these transcription factors to the radiolabeled BMP-RE2/bZIP/HNF4α/COUP probe. Binding to a probe encompassing a MEL motif was blocked by the addition of cold competitor to C/EBPα and could be supershifted with antibodies against C/EBPα. In conclusion, SMAD 3/4, COUP-Tf, HNF4α, C/EBPα, GATA2 and STAT5 appear to be important in the regulation of Hamp1 expression.

scholarly journals Mouse BTEB3, a new member of the basic transcription element binding protein (BTEB) family, activates expression from GC-rich minimal promoter regions

2000 ◽  
Vol 345 (3) ◽  
pp. 529-533 ◽  
Author(s):  
Karen M. MARTIN ◽  
Wendy N. COOPER ◽  
James C. METCALFE ◽  
Paul R. KEMP
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Zinc Finger ◽  
Binding Protein ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Minimal Promoter ◽  
Promoter Regions ◽  
Basal Transcription ◽  
Element Binding Protein

Members of the three-zinc-finger family of transcription factors play an important role in determining basal transcription. We have cloned mouse BTEB3 (mBTEB3), a new member of the basic transcription element binding protein (BTEB) family, which is expressed in a wide variety of tissues. mBTEB3 activates transcription of the simian virus 40 early promoter (4-fold) and of the tissue-specific SM22α promoter (100-fold), suggesting that, like BTEB1 and Sp1, mBTEB3 is a basal transcription factor.

Analysis of transcription factors binding to the human 7SL RNA gene promoter

1999 ◽  
Vol 77 (5) ◽  
pp. 431-438 ◽  
Author(s):  
Jürgen Müller ◽  
Bernd-Joachim Benecke
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Gene Promoter ◽  
7Sl Rna ◽  
Polymerase Iii ◽  
Responsive Element

Transcription of the human 7SL RNA gene by RNA polymerase III depends on the concerted action of transcription factors binding to the gene-internal and gene-external parts of its promoter. Here, we investigated which transcription factors interact with the human 7SL RNA gene promoter and which are required for transcription of the human 7SL RNA gene. A-box/B-box elements were previously identified in 5S RNA, tRNA, and virus associated RNA genes and are recognized by transcription factor IIIC (TFIIIC). The gene-internal promoter region of the human 7SL RNA gene shows only limited similarity to those elements. Nevertheless, competition experiments and the use of highly enriched factor preparations demonstrate that TFIIIC is required for human 7SL transcription. The gene-external part of the promoter includes an authentic cAMP-responsive element previously identified in various RNA polymerase II promoters. Here we demonstrate that members of the activating transcription factor/cyclic AMP-responsive element binding protein (ATF/CREB) transcription factor family bind specifically to this element in vitro. However, the human 7SL RNA gene is not regulated by cAMP in vivo. Furthermore, in vitro transcription of the gene does not depend on ATF/CREB transcription factors. It rather appears that a transcription factor with DNA-binding characteristics like ATF/CREB proteins but otherwise different properties is required for human 7SL RNA transcription.Key words: 7SL RNA, ATF, CRE, TFIIIC, RNA polymerase III.

scholarly journals Transcription Factors and Methylation Drive Prognostic miRNA Dysregulation in Hepatocellular Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Shijie Qin ◽  
Jieyun Xu ◽  
Yunmeng Yi ◽  
Sizhu Jiang ◽  
Ping Jin ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Tumor Suppressor ◽  
Tumor Suppressors ◽  
Tumor Suppressor Genes ◽  
Mature Mirnas ◽  
Promoter Regions ◽  
Multiple Tumor ◽  
Tumor Suppressor Mirnas ◽  
Abnormal Cell Proliferation

Many dysregulated microRNAs (miRNAs) have been suggested to serve as oncogenes or tumor suppressors to act as diagnostic and prognostic factors for HCC patients. However, the dysregulated mechanisms of miRNAs in HCC remain largely unknown. Herein, we firstly identify 114 disordered mature miRNAs in HCC, 93 of them are caused by dysregulated transcription factors, and 10 of them are driven by the DNA methylation of their promoter regions. Secondly, we find that seven up-regulated miRNAs (miR-9-5p, miR-452-5p, miR-452-3p, miR-1180-3p, miR-4746-5p, miR-3677-3 and miR-4661-5p) can promote tumorigenesis via inhibiting multiple tumor suppressor genes participated in metabolism, which may act as oncogenes, and seven down-regulated miRNAs (miR-99-5p, miR-5589-5p, miR-5589-3p, miR-139-5p, miR-139-3p, miR-101-3p and miR-125b-5p) can suppress abnormal cell proliferation via suppressing a number of oncogenes involved in cancer-related pathways, which may serve as tumor suppressors. Thirdly, our findings reveal a mechanism that transcription factor and miRNA interplay can form various regulatory loops to synergistically control the occurrence and development of HCC. Finally, our results demonstrate that this key transcription factor FOXO1 can activate a certain number of tumor suppressor miRNAs to improve the survival of HCC patients, suggesting FOXO1 as an effective therapeutic target for HCC patients. Overall, our study not only reveals the dysregulated mechanisms of miRNAs in HCC, but provides several novel prognostic biomarkers and potential therapeutic targets for HCC patients.

Transcription factors in mouse lung development and function

2001 ◽  
Vol 280 (5) ◽  
pp. L823-L838 ◽  
Author(s):  
Robert H. Costa ◽  
Vladimir V. Kalinichenko ◽  
Lorena Lim
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Cellular Proliferation ◽  
Developmental Process ◽  
Circulatory System ◽  
Branching Morphogenesis ◽  
Mouse Lung ◽  
Promoter Regions ◽  
Major Function

Development of the mouse lung initiates on day 9.5postcoitum from the laryngotracheal groove and involves mesenchymal-epithelial interactions, in particular, those between the splanchnic mesoderm and epithelial cells (derived from foregut endoderm) that induce cellular proliferation, migration, and differentiation, resulting in branching morphogenesis. This developmental process mediates formation of the pulmonary bronchiole tree and integrates a terminal alveolar region with an extensive endothelial capillary bed, which facilitates efficient gas exchange with the circulatory system. The major function of the mesenchymal-epithelial signaling is to potentiate the activity or expression of cell type-specific transcription factors in the developing lung, which, in turn, cooperatively bind to distinct promoter regions and activate target gene expression. In this review, we focus on the role of transcription factors in lung morphogenesis and the maintenance of differentiated gene expression. These lung transcription factors include forkhead box A2 [also known as hepatocyte nuclear factor (HNF)-3β], HNF-3/forkhead homolog (HFH)-8 [also known as FoxF1 or forkhead-related activator-1], HNF-3/forkhead homolog-4 (also known as FoxJ1), thyroid transcription factor-1 (Nkx2.1), and homeodomain box A5 transcription factors, the zinc finger Gli (mouse homologs of the Drosophila cubitus interruptus) and GATA transcription factors, and the basic helix-loop-helix Pod1 transcription factor. We summarize the phenotypes of transgenic and knockout mouse models, which define important functions of these transcription factors in cellular differentiation and lung branching morphogenesis.

scholarly journals Cellular Phosphorylation Signaling and Gene Expression in Drought Stress Responses: ABA-Dependent and ABA-Independent Regulatory Systems

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 756
Author(s):  
Fumiyuki Soma ◽  
Fuminori Takahashi ◽  
Kazuko Yamaguchi-Shinozaki ◽  
Kazuo Shinozaki
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Drought Stress ◽  
Plant Growth ◽  
Protein Kinases ◽  
Stress Responses ◽  
Regulatory Pathways ◽  
Cis Acting ◽  
Regulatory Systems ◽  
Responsive Element

Drought is a severe and complex abiotic stress that negatively affects plant growth and crop yields. Numerous genes with various functions are induced in response to drought stress to acquire drought stress tolerance. The phytohormone abscisic acid (ABA) accumulates mainly in the leaves in response to drought stress and then activates subclass III SNF1-related protein kinases 2 (SnRK2s), which are key phosphoregulators of ABA signaling. ABA mediates a wide variety of gene expression processes through stress-responsive transcription factors, including ABA-RESPONSIVE ELEMENT BINDING PROTEINS (AREBs)/ABRE-BINDING FACTORS (ABFs) and several other transcription factors. Seed plants have another type of SnRK2s, ABA-unresponsive subclass I SnRK2s, that mediates the stability of gene expression through the mRNA decay pathway and plant growth under drought stress in an ABA-independent manner. Recent research has elucidated the upstream regulators of SnRK2s, RAF-like protein kinases, involved in early responses to drought stress. ABA-independent transcriptional regulatory systems and ABA-responsive regulation function in drought-responsive gene expression. DEHYDRATION RESPONSIVE ELEMENT (DRE) is an important cis-acting element in ABA-independent transcription, whereas ABA-RESPONSIVE ELEMENT (ABRE) cis-acting element functions in ABA-responsive transcription. In this review article, we summarize recent advances in research on cellular and molecular drought stress responses and focus on phosphorylation signaling and transcription networks in Arabidopsis and crops. We also highlight gene networks of transcriptional regulation through two major regulatory pathways, ABA-dependent and ABA-independent pathways, that ABA-responsive subclass III SnRK2s and ABA-unresponsive subclass I SnRK2s mediate, respectively. We also discuss crosstalk in these regulatory systems under drought stress.

scholarly journals Genome-wide identification and function analysis of ERF2 gene family in response to disease resistance against Stemphylium lycopersici in tomato

2020 ◽  
Author(s):  
Huanhuan Yang ◽  
Yaoguang Sun ◽  
Hexuan Wang ◽  
Jingbin Jiang ◽  
Jingfu Li
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Disease Resistance ◽  
Function Analysis ◽  
Virus Induced Gene Silencing ◽  
Biotic And Abiotic Stress ◽  
Specific Expression ◽  
Stemphylium Lycopersici ◽  
Erf Family ◽  
Erf Transcription Factor

Abstract Background APETALA2/ethylene responsive factor (AP2/ERF) transcription factors are a plant-specific family of transcription factors and one of the largest families of transcription factors. Ethylene response factors (ERFs) regulate plant growth, development, and responses to biotic and abiotic stress. In a previous study, the ERF2 gene was significantly upregulated in both resistant and susceptible tomato cultivars in response to Stemphylium lycopersici. The main purpose of this study is to systematically analyze the ERF family and to explore the mechanism of ERF2 in tomato plants resisting pathogen infection by Virus-induced Gene Silencing (VIGS) technique. Results In this experiment, 134 ERF genes were excavated and subjected to bioinformatic analysis. This experiment divided 134 ERF members into twelve groups based on the conserved domain of the genes. Specific expression of the tomato ERF transcription factor family genes in different organs. Combined with RNA-seq, we found that the expression of 18 ERF transcription factor increased after inoculation with S. lycopersici. In ERF2-silenced plants, the susceptible phenotype was observed after inoculation with S. lycopersici. The hypersensitive response and ROS production were decreased in the silenced ERF2 plants. Physiological analyses showed that the superoxide dismutase, peroxidase and catalase activities were lower in ERF2-silenced plants than in control plants, and the SA and JA contents were lower in ERF2-silenced plants than in control plants after inoculation with S. lycopersici. Furthermore, the results indicated that ERF2 may directly or indirectly regulate Pto, PR1b1 and PR-P2 expression and enhance tomato resistance. Conclusions In this study, we identified and analyzed the members of tomato ERF family by bioinformatics methods, and classified, described and analyzed these genes. we found that ERF2 was positively regulated tomato resistance to S. lycopersici by VIGS. Interestingly, ERF2 played a key role in multiple SA, JA and ROS signaling pathways to confer resistance to invasion by S. lycopersici. In addition, ERF2may directly or indirectly regulate Pto, PR1b1 and PR-P2 expression and enhance tomato resistance to S. lycopersici. In summary, this study provides gene resources for breeding for disease resistance in tomato.

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