scholarly journals Bacterium-Enabled Transient Gene Activation by Artificial Transcription Factor for Resolving Gene Regulation in Maize

2021 ◽  
Author(s):  
Mingxia Zhao ◽  
Zhao Peng ◽  
Yang Qin ◽  
Ling Zhang ◽  
Bin Tian ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Protein Delivery ◽  
Graphical Model ◽  
Gene Activation ◽  
Cuticular Wax ◽  
Host Cells ◽  
Myb Transcription Factor ◽  
Leaf Phenotype

ABSTRACTCellular functions are diversified through intricate transcription regulations, and an understanding gene regulation networks is essential to elucidating many developmental processes and environmental responses. Here, we employed the Transcriptional-Activator Like effectors (TALes), which represent a family of transcription factors that are synthesized by members of the γ-proteobacterium genus Xanthomonas and secreted to host cells for activation of targeted host genes. Through delivery by the maize pathogen, Xanthomonas vasicola pv. vasculorum, designer TALes (dTALes), which are synthetic TALes, were used to induce the expression of the maize gene glossy3 (gl3), a MYB transcription factor gene involved in the cuticular wax biosynthesis. RNA-Seq analysis of leaf samples identified 146 gl3 downstream genes. Eight of the nine known genes known to be involved in the cuticular wax biosynthesis were up-regulated by at least one dTALe. A top-down Gaussian graphical model predicted that 68 gl3 downstream genes were directly regulated by GL3. A chemically induced mutant of the gene Zm00001d017418 from the gl3 downstream gene, encoding aldehyde dehydrogenase, exhibited a typical glossy leaf phenotype and reduced epicuticular waxes. The bacterial protein delivery of artificial transcription factors, dTALes, proved to be a straightforward and powerful approach for the revelation of gene regulation in plants.

scholarly journals Comprehensive influences of overexpression of a MYB transcriptor regulating anthocyanin biosynthesis on transcriptome and metabolome of tobacco leaves

2019 ◽  
Author(s):  
Yuan Zong ◽  
Shiming Li ◽  
Xingyuan Xi ◽  
Dong Cao ◽  
Zhong Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Anthocyanin Biosynthesis ◽  
Chemical Compounds ◽  
Myb Transcription Factor ◽  
Biosynthesis Pathway ◽  
Structural Genes ◽  
Leaf Phenotype ◽  
Transgenic Lines ◽  
Purple Leaf

Abstract Background Overexpression of MYB transcription factors can induce the expression of structural genes for anthocyanin biosynthesis and increase the anthocyanin content of plant tissues. However, it remains unclear whether MYB transcription factor overexpression effects the activation of other genes and the concomitant accumulation of chemical compounds. Results Overexpression of LrAN2 promoted anthocyanin accumulation in a variety of tissues in tobacco cultivar Samsun. Only 185 unigenes, from total of 160,965, were expressed differently in leaves and 241 chemical compounds exhibited differences in accumulation. Four anthocyanins, including apigeninidin chloride, cyanidin 3-O-malonylhexoside, pelargonidin 3-O-beta-D-glucoside, and cyanidin 3,5-O-diglucoside were detected only in transgenic lines, which could explain the purple leaf phenotype. Beside anthocyanins, the phenylpropanoids, polyphenols (catechins), flavonoids, flavones, and flavonols were also upregulated. Overexpression of LrAN2 activated the basic helix-loop-helix transcription factor AN1b, and the MYB transcription factor MYB3. Additionally, structural genes associated with the phenylpropanoid biosynthetic pathway were activated, which lead to the upregulated accumulation of phenylpropanoid, polyphenol (catechin), flavonoid, flavone, flavonol, and anthocyanin. The MYB transcription factor CPC, a negative regulator of anthocyanin biosynthesis, was also expressed at increased levels in transgenic lines, which implie that a negative regulation mechanism existed in the anthocyanin biosynthesis pathway. The relative contents of all 19 differently accumulated amino groups and derivatives were decreased in transgenic lines, which meant that the phenylalanine biosynthesis pathway used other amino acids as substrates. Interestingly, the expression of acetylalkylglycerol acetylhydrolase was suppressed in transgenic lines, which caused the accumulation of 19 lyso-phosphatidylcholine derivatives and a decrease in production of eight octodecane derivatives. Conclusions Overexpression of LrAN2 activates the pathway of anthocyanin synthesis and metabolism in tobacco. Four anthocyanins lead to the purple leaf phenotype The main pathways of flavonoid biosynthesis were up-regulated. This research provides more information about the function of MYB transcription factors in anthocyanin biosynthesis and the production of other chemical compounds. This work will help breeders to obtain new plant cultivars with high anthocyanin contents using biotechnology.

scholarly journals Identification of MEF2-regulated genes during muscle differentiation

2004 ◽  
Vol 20 (1) ◽  
pp. 143-151 ◽  
Author(s):  
James Paris ◽  
Carl Virtanen ◽  
Zhibin Lu ◽  
Mark Takahashi
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Neuromuscular Junctions ◽  
Muscle Differentiation ◽  
Signaling Cascades ◽  
Specific Gene ◽  
Genetic Mechanisms ◽  
Selection Parameters ◽  
First Time

Although a great deal has been elucidated concerning the mechanisms regulating muscle differentiation, little is known about transcription factor-specific gene regulation. Our understanding of the genetic mechanisms regulating cell differentiation is quite limited. Much of what has been defined centers on regulatory signaling cascades and transcription factors. Surprisingly few studies have investigated the association of genes with specific transcription factors. To address these issues, we have utilized a method coupling chromatin immunoprecipitation and CpG microarrays to characterize the genes associated with MEF2 in differentiating C2C12 cells. Results demonstrated a defined binding pattern over the course of differentiation. Filtered data demonstrated 9 clones to be elevated at 0 h, 792 at 6 h, 163 by 1 day, and 316 at 3 days. Using unbiased selection parameters, we selected a subset of 291 prospective candidates. Clones were sequenced and filtered for removal of redundancy between clones and for the presence of repetitive elements. We were able to place 50 of these on the mouse genome, and 20 were found to be located near well-annotated genes. From this list, previously undefined associations with MEF2 were discovered. Many of these genes represent proteins involved in neurogenesis, neuromuscular junctions, signaling and metabolism. The remaining clones include many full-length cDNA and represent novel gene targets. The results of this study provides for the first time, a unique look at gene regulation at the level of transcription factor binding in differentiating muscle.

scholarly journals Expression of MYB transcription factor gene ZmMYB59 affects seed germination in Nicotiana tabacum and Oryza sativa

2020 ◽  
Author(s):  
Kaihui Zhai ◽  
Guangwu Zhao ◽  
Hongye Jiang ◽  
Caixia Sun ◽  
Jingyu Ren
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Seed Germination ◽  
Transgenic Tobacco ◽  
Germination Rate ◽  
Myb Transcription Factor ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Myb Transcription Factors ◽  
Vigor Index

Abstract Background MYB transcription factors are involved in many biological processes, including metabolism, development and responses to biotic and abiotic stresses. In our previous work, a new MYB transcription factor gene, ZmMYB59 was induced by deep sowing and down-regulated during maize seed germination via Real-Time PCR. However, there are few reports on seed germination regulated by MYB proteins and the functions of ZmMYB59 remain unknown. Results In this study, to examine its functions, Agrobacterium -mediated transformation was exploited to generate ZmMYB59 transgenic tobacco and rice. In T 2 generation transgenic tobacco, germination rate, germination index, vigor index and hypocotyl length were significantly decreased by 25.0~50.9%, 34.5~54.4%, 57.5~88.3% and 21.9~31.2% compared to wild-type (WT) lines. In T 2 generation transgenic rice, germination rate, germination index, vigor index and mesocotyl length were notably reduced by 39.1~53.8%, 51.4~71.4%, 52.5~74.0% and 28.3~41.5%, respectively. On this basis, relative physiological indicators were determined. The activities of catalase, peroxidase, superoxide dismutase, ascorbate peroxidase and proline content of transgenic lines were significantly lower than those of WT, suggesting that ZmMYB59 reduced their antioxidant capacity. As well, ZmMYB59 expression extremely inhibited the synthesis of gibberellin A1 (GA 1 ) and cytokinin (CTK), and promoted the synthesis of abscisic acid (ABA) concurrently, which implied that seed germination was repressed by ZmMYB59 in hormone levels. Furthermore, cell length and cell number of hypocotyl/mesocotyl in transgenic plants were notably decreased. Conclusions Taken together, it proposed that ZmMYB59 plays a negative regulation during seed germination in tobacco and rice, which also contributes to illuminate the molecular mechanisms regulated by MYB transcription factors.

scholarly journals A Role for Mediator Core in Limiting Coactivator Recruitment in Saccharomyces cerevisiae

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 407-420 ◽  
Author(s):  
Robert M. Yarrington ◽  
Yaxin Yu ◽  
Chao Yan ◽  
Lu Bai ◽  
David J. Stillman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Gene Activation ◽  
Mediator Complex ◽  
Transcriptional Coactivator ◽  
The Core ◽  
Link Type ◽  
Upstream Activating Sequence ◽  
Eukaryotic Organisms

Mediator is an essential, multisubunit complex that functions as a transcriptional coactivator in yeast and other eukaryotic organisms. Mediator has four conserved modules, Head, Middle, Tail, and Kinase, and has been implicated in nearly all aspects of gene regulation. The Tail module has been shown to recruit the Mediator complex to the enhancer or upstream activating sequence (UAS) regions of genes via interactions with transcription factors, and the Kinase module facilitates the transition of Mediator from the UAS/enhancer to the preinitiation complex via protein phosphorylation. Here, we analyze expression of the Saccharomyces cerevisiae HO gene using a sin4 Mediator Tail mutation that separates the Tail module from the rest of the complex; the sin4 mutation permits independent recruitment of the Tail module to promoters without the rest of Mediator. Significant increases in recruitment of the SWI/SNF and SAGA coactivators to the HO promoter UAS were observed in a sin4 mutant, along with increased gene activation. These results are consistent with recent studies that have suggested that the Kinase module functions negatively to inhibit activation by the Tail. However, we found that Kinase module mutations did not mimic the effect of a sin4 mutation on HO expression. This suggests that at HO the core Mediator complex (Middle and Head modules) must play a role in limiting Tail binding to the promoter UAS and gene activation. We propose that the core Mediator complex helps modulate Mediator binding to the UAS regions of genes to limit coactivator recruitment and ensure proper regulation of gene transcription.

scholarly journals Modulation of Pseudomonas aeruginosa Quorum Sensing by Glutathione

2019 ◽  
Vol 201 (9) ◽  
Author(s):  
Hui Zhou ◽  
Meizhen Wang ◽  
Nicole E. Smalley ◽  
Maxim Kostylev ◽  
Amy L. Schaefer ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Quorum Sensing ◽  
Cell Density ◽  
Redox State ◽  
Gene Activation ◽  
Cellular Redox ◽  
Content Type ◽  
Cellular Redox State

ABSTRACT Pseudomonas aeruginosa uses quorum sensing (QS) to regulate the production of a battery of secreted products. At least some of these products are shared among the population and serve as public goods. When P. aeruginosa is grown on casein as the sole carbon and energy source, the QS-induced extracellular protease elastase is required for growth. We isolated a P. aeruginosa variant, which showed increased production of QS-induced factors after repeated transfers in casein broth. This variant, P. aeruginosa QS*, had a mutation in the glutathione synthesis gene gshA. We describe several experiments that show a gshA coding variant and glutathione affect the QS response. The P. aeruginosa QS transcription factor LasR has a redox-sensitive cysteine (C79). We report that GshA variant cells with a LasR C79S substitution show a similar QS response to that of wild-type P. aeruginosa. Surprisingly, it is not LasR but the QS transcription factor RhlR that is more active in bacteria containing the variant gshA. Our results demonstrate that QS integrates information about cell density and the cellular redox state via glutathione levels. IMPORTANCE Pseudomonas aeruginosa and other bacteria coordinate group behaviors using a chemical communication system called quorum sensing (QS). The QS system of P. aeruginosa is complex, with several regulators and signals. We show that decreased levels of glutathione lead to increased gene activation in P. aeruginosa, which did not occur in a strain carrying the redox-insensitive variant of a transcription factor. The ability of P. aeruginosa QS transcription factors to integrate information about cell density and cellular redox state shows these transcription factors can fine-tune levels of the gene products they control in response to at least two types of signals or cues.

scholarly journals The transcription factor TAL1 and miR-17-92 create a regulatory loop in hematopoiesis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Annekarin Meyer ◽  
Stefanie Herkt ◽  
Heike Kunze-Schumacher ◽  
Nicole Kohrs ◽  
Julia Ringleb ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Malignant Disease ◽  
Expression Patterns ◽  
Gene Activation ◽  
Erythroid Differentiation ◽  
Mature Micrornas ◽  
Gene Regulatory ◽  
Regulatory Loop ◽  
Transcriptional Complex

AbstractA network of gene regulatory factors such as transcription factors and microRNAs establish and maintain gene expression patterns during hematopoiesis. In this network, transcription factors regulate each other and are involved in regulatory loops with microRNAs. The microRNA cluster miR-17-92 is located within the MIR17HG gene and encodes six mature microRNAs. It is important for hematopoietic differentiation and plays a central role in malignant disease. However, the transcription factors downstream of miR-17-92 are largely elusive and the transcriptional regulation of miR-17-92 is not fully understood. Here we show that miR-17-92 forms a regulatory loop with the transcription factor TAL1. The miR-17-92 cluster inhibits expression of TAL1 and indirectly leads to decreased stability of the TAL1 transcriptional complex. We found that TAL1 and its heterodimerization partner E47 regulate miR-17-92 transcriptionally. Furthermore, miR-17-92 negatively influences erythroid differentiation, a process that depends on gene activation by the TAL1 complex. Our data give example of how transcription factor activity is fine-tuned during normal hematopoiesis. We postulate that disturbance of the regulatory loop between TAL1 and the miR-17-92 cluster could be an important step in cancer development and progression.

scholarly journals CmMYB#7, an R3 MYB transcription factor, acts as a negative regulator of anthocyanin biosynthesis in chrysanthemum

2019 ◽  
Vol 70 (12) ◽  
pp. 3111-3123 ◽  
Author(s):  
Lili Xiang ◽  
Xiaofen Liu ◽  
Heng Li ◽  
Xueren Yin ◽  
Donald Grierson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Site ◽  
Transient Expression ◽  
Regulatory Mechanism ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Negative Regulator ◽  
Myb Transcription Factor ◽  
Anthocyanin Content

Abstract ‘Jimba’, a well-known white flowered chrysanthemum cultivar, occasionally and spontaneously produces red colored petals under natural cultivation, but there is little information about the molecular regulatory mechanism underlying this process. We analysed the expression patterns of 91 MYB transcription factors in ‘Jimba’ and ‘Turning red Jimba’ and identified an R3 MYB, CmMYB#7, whose expression was significantly decreased in ‘Turning red Jimba’ compared with ‘Jimba’, and confirmed it is a passive repressor of anthocyanin biosynthesis. CmMYB#7 competed with CmMYB6, which together with CmbHLH2 is an essential component of the anthocyanin activation complex, for interaction with CmbHLH2 through the bHLH binding site in the R3 MYB domain. This reduced binding of the CmMYB6–CmbHLH2 complex and inhibited its ability to activate CmDFR and CmUFGT promoters. Moreover, using transient expression assays we demonstrated that changes in the expression of CmMYB#7 accounted for alterations in anthocyanin content. Taken together, our findings illustrate that CmMYB#7 is a negative regulator of anthocyanin biosynthesis in chrysanthemum.

WOOLLY, interacting with MYB transcription factor MYB31, regulates cuticular wax biosynthesis by modulating CER6 expression in tomato

2020 ◽  
Vol 103 (1) ◽  
pp. 323-337 ◽  
Author(s):  
Cheng Xiong ◽  
Qingmin Xie ◽  
Qihong Yang ◽  
Pengya Sun ◽  
Shenghua Gao ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Cuticular Wax ◽  
Myb Transcription Factor

GATA-1 Forms Distinct Activating and Repressive Complexes in Erythroid Cells.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 356-356
Author(s):  
John Strouboulis ◽  
Patrick Rodriguez ◽  
Edgar Bonte ◽  
Jeroen Krijgsveld ◽  
Katarzyna Kolodziej ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Chromatin Remodeling ◽  
Gene Activation ◽  
Erythroid Differentiation ◽  
Specific Gene ◽  
Erythroid Cells ◽  
In Erythroid Cells

Abstract GATA-1 is a key transcription factor essential for the differentiation of the erythroid, megakaryocytic and eosinophilic lineages. GATA-1 functions in erythropoiesis involve lineage-specific gene activation and repression of early hematopoietic transcription programs. GATA-1 is known to interact with other transcription factors, such as FOG-1, TAL-1 and Sp1 and also with CBP/p300 and the SWI/SNF chromatin remodeling complex in vitro. Despite this information the molecular basis of its essential functions in erythropoiesis remains unclear. We show here that GATA-1 is mostly present in a high (> 670kDa) molecular weight complex that appears to be dynamic during erythroid differentiation. In order to characterize the GATA-1 complex(es) from erythroid cells, we employed an in vivo biotinylation tagging approach in mouse erythroleukemic (MEL) cells1. Briefly, this involved the fusion of a small (23aa) peptide tag to GATA-1 and its specific, efficient biotinylation by the bacterial BirA biotin ligase which is co-expressed with tagged GATA-1 in MEL cells. Nuclear extracts expressing biotinylated tagged GATA-1 were bound directly to streptavidin beads and co-purifying proteins were identified by mass spectrometry. In addition to the known GATA-1-interacting transcription factors FOG-1, TAL-1 and Ldb-1, we describe novel interactions with the essential hematopoietic transcription factor Gfi-1b and the chromatin remodeling complexes MeCP1 and ACF/WCRF. Significantly, GATA-1 interaction with the repressive MeCP1 complex requires FOG-1. We also show in erythroid cells that GATA-1, FOG-1 and MeCP1 are stably bound to repressed genes representing early hematopoietic (e.g. GATA-2) or alternative lineage-specific (e.g. eosinophilic) transcription programs, whereas the GATA-1/Gfi1b complex is bound to repressed genes involved in cell proliferation. In contrast, GATA-1 and TAL-1 are bound to the active erythroid-specific EKLF gene. Our findings on GATA-1 complexes provide novel insight as to the critical roles that GATA-1 plays in many aspects of erythropoiesis by revealing the GATA-1 partners in the execution of specific functions.

scholarly journals Regulating the Regulators: The Role of Histone Deacetylase 1 (HDAC1) in Erythropoiesis

2020 ◽  
Vol 21 (22) ◽  
pp. 8460
Author(s):  
Min Young Kim ◽  
Bowen Yan ◽  
Suming Huang ◽  
Yi Qiu
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Histone Deacetylase ◽  
Histone Deacetylases ◽  
Gene Activation ◽  
Bhlh Transcription Factor ◽  
Nucleosome Remodeling ◽  
Hdac Activity ◽  
Histone Deacetylase 1

Histone deacetylases (HDACs) play important roles in transcriptional regulation in eukaryotic cells. Class I deacetylase HDAC1/2 often associates with repressor complexes, such as Sin3 (Switch Independent 3), NuRD (Nucleosome remodeling and deacetylase) and CoREST (Corepressor of RE1 silencing transcription factor) complexes. It has been shown that HDAC1 interacts with and modulates all essential transcription factors for erythropoiesis. During erythropoiesis, histone deacetylase activity is dramatically reduced. Consistently, inhibition of HDAC activity promotes erythroid differentiation. The reduction of HDAC activity not only results in the activation of transcription activators such as GATA-1 (GATA-binding factor 1), TAL1 (TAL BHLH Transcription Factor 1) and KLF1 (Krüpple-like factor 1), but also represses transcription repressors such as PU.1 (Putative oncogene Spi-1). The reduction of histone deacetylase activity is mainly through HDAC1 acetylation that attenuates HDAC1 activity and trans-repress HDAC2 activity through dimerization with HDAC1. Therefore, the acetylation of HDAC1 can convert the corepressor complex to an activator complex for gene activation. HDAC1 also can deacetylate non-histone proteins that play a role on erythropoiesis, therefore adds another layer of gene regulation through HDAC1. Clinically, it has been shown HDACi can reactivate fetal globin in adult erythroid cells. This review will cover the up to date research on the role of HDAC1 in modulating key transcription factors for erythropoiesis and its clinical relevance.

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