scholarly journals Genome-wide analysis of transcription factors related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8041
Author(s):  
Jian Gao ◽  
Hua Peng ◽  
Fabo Chen ◽  
Mao Luo ◽  
Wenbo Li
Keyword(s):  
Transcription Factors ◽  
Anthocyanin Biosynthesis ◽  
Red Pigment ◽  
Sequencing Data ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Genome Wide ◽  
Important Regulator ◽  
Regulatory Model ◽  
Red Radish

Carmine radish produced in Chongqing is famous for containing a natural red pigment (red radish pigment). However, the anthocyanin biosynthesis transcriptome and the expression of anthocyanin biosynthesis-related genes in carmine radish have not been fully investigated. Uncovering the mechanism of anthocyanin biosynthesis in the ‘Hongxin 1’ carmine radish cultivar has become a dominant research topic in this field. In this study, a local carmine radish cultivar named ‘Hongxin 1’ containing a highly natural red pigment was used to analyze transcription factors (TFs) related to anthocyanin biosynthesis during the dynamic development of fleshy roots. Based on RNA sequencing data, a total of 1,747 TFs in 64 TF families were identified according to their DNA-binding domains. Of those, approximately 71 differentially expressed transcription factors (DETFs) were commonly detected in any one stage compared with roots in the seedling stage (SS_root). Moreover, 26 transcripts of DETFs targeted by 74 miRNAs belonging to 25 miRNA families were identified, including MYB, WRKY, bHLH, ERF, GRAS, NF-YA, C2H2-Dof, and HD-ZIP. Finally, eight DETF transcripts belonging to the C2C2-Dof, bHLH and ERF families and their eight corresponding miRNAs were selected for qRT-PCR to verify their functions related to anthocyanin biosynthesis during the development of carmine radish fleshy roots. Finally, we propose a putative miRNA-target regulatory model associated with anthocyanin biosynthesis in carmine radish. Our findings suggest that sucrose synthase might act as an important regulator to modulate anthocyanin biosynthesis in carmine radish by inducing several miRNAs (miR165a-5p, miR172b, miR827a, miR166g and miR1432-5p) targeting different ERFs than candidate miRNAs in the traditional WMBW complex in biological processes.

scholarly journals Editing of the MYB genes in Brassica napus as a method to increase anthocyanin pigmentation and stress tolerance

2020 ◽  
Vol 224 ◽  
pp. 04022
Author(s):  
E V Mikhaylova ◽  
M. Y. Shein ◽  
A. Y. Artyukhin ◽  
A S Sukhareva ◽  
M. A. Panfilova ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Brassica Napus ◽  
Genome Editing ◽  
Anthocyanin Biosynthesis ◽  
Phytopathogenic Fungi ◽  
Anthocyanin Pigmentation ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Myb Genes ◽  
Genetic Constructs

Anthocyanin hyperaccumulation is an important agricultural trait, associated with resistance to abiotic stress, pests, phytopathogenic fungi and bacterial diseases. B. napus with increased anthocyanin pigmentation can be generated by genome editing. Many transcription factors of the MYB family are involved in stress response and anthocyanin biosynthesis. Genes AtMYB60, AtCPC and AtMYBL2 are negative regulators of anthocyanin biosynthesis in Arabidopsis, therefore the knockout of these genes can result in increased anthocyanin pigmentation. gRNA spacers were synthesized to target the orthologs of these genes, identified in Brassica napus. Resulting genetic constructs were introduced to the plant tissues by agroinfiltration. Transient expression of gRNAs targeting DNA-binding domains of MYB transcription factors along with Cas9 nuclease successfully promoted anthocyanin hyperaccumulation. These genetic constructs can be used for genome editing and production of new colored and stress tolerant varieties of oilseed rape.

scholarly journals Mechanistic Heterogeneity in Site Recognition by the Structurally Homologous DNA-binding Domains of the ETS Family Transcription Factors Ets-1 and PU.1

2014 ◽  
Vol 289 (31) ◽  
pp. 21605-21616 ◽  
Author(s):  
Shuo Wang ◽  
Miles H. Linde ◽  
Manoj Munde ◽  
Victor D. Carvalho ◽  
W. David Wilson ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Ets Family ◽  
Site Recognition

scholarly journals Msn2- and Msn4-Like Transcription Factors Play No Obvious Roles in the Stress Responses of the Fungal Pathogen Candida albicans

2004 ◽  
Vol 3 (5) ◽  
pp. 1111-1123 ◽  
Author(s):  
Susan Nicholls ◽  
Melissa Straffon ◽  
Brice Enjalbert ◽  
André Nantel ◽  
Susan Macaskill ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Transcription Factors ◽  
Stress Responses ◽  
Ectopic Expression ◽  
Heavy Metal Stress ◽  
Luciferase Reporter ◽  
Response Element ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Adverse Environmental Conditions

ABSTRACT In Saccharomyces cerevisiae, the (C2H2)2 zinc finger transcription factors Msn2 and Msn4 play central roles in responses to a range of stresses by activating gene transcription via the stress response element (STRE; CCCCT). The pathogen Candida albicans displays stress responses that are thought to help it survive adverse environmental conditions encountered within its human host. However, these responses differ from those in S. cerevisiae, and hence we predicted that the roles of Msn2- and Msn4-like proteins might have been functionally reassigned in C. albicans. C. albicans has two such proteins: CaMsn4 and Mnl1 (for Msn2- and Msn4-like). CaMSN4, but not MNL1, weakly complemented the inability of an S. cerevisiae msn2 msn4 mutant to activate a STRE-lacZ reporter. Also, the disruption of CaMsn4 and Mnl1 had no discernible effect upon the resistance of C. albicans to heat, osmotic, ethanol, nutrient, oxidative, or heavy-metal stress or upon the stress-activated transcriptome in C. albicans. Furthermore, although Cap1-dependent activation of a Yap response element-luciferase reporter was observed, a STRE reporter was not activated in response to stresses in C. albicans. Ectopic expression of CaMsn4 or Mnl1 did not affect the cellular or molecular responses of C. albicans to stress. Under the conditions tested, the putative activation and DNA binding domains of CaMsn4 did not appear to be functional. These data suggest that CaMsn4 and Mnl1 do not contribute significantly to stress responses in C. albicans. The data are consistent with the idea that stress signaling in this fungus has diverged significantly from that in budding yeast.

scholarly journals Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638

Life ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 40 ◽  
Author(s):  
Antonia Denis ◽  
Mario Alberto Martínez-Núñez ◽  
Silvia Tenorio-Salgado ◽  
Ernesto Perez-Rueda
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Regulatory Networks ◽  
Pyrococcus Furiosus ◽  
Structural Domain ◽  
Transcriptional Regulatory Networks ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Transcriptional Regulatory ◽  
Cellular Domain

In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.

Dimeric transcription factor families: it takes two to tango but who decides on partners and the venue?

1992 ◽  
Vol 103 (1) ◽  
pp. 9-14 ◽  
Author(s):  
K.A. Lee
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Experimental Evidence ◽  
Cdna Cloning ◽  
Transcriptional Activation ◽  
Effector Functions ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Elements

Dimeric transcription factors that bind to DNA are often grouped into families on the basis of dimerization and DNA-binding specificities. cDNA cloning studies have established that members of the same family have structurally related dimerisation and DNA-binding domains but diverge in other regions that are important for transcriptional activation. These features lead to the straightforward suggestion that although all members of a family bind to similar DNA elements, individual members exhibit distinct transcriptional effector functions. This simple view is now supported by experimental evidence from those systems that have proved amenable to study. There are however some largely unaddressed questions that concern the mechanisms that allow family members to go about their business without interference from their highly related siblings. Here I will discuss some insights from studies of the bZIP class of transcription factors.

Biologic significance of GATA-1 activities in Ras-mediated megakaryocytic differentiation of hematopoietic cell lines

Blood ◽  
2000 ◽  
Vol 96 (7) ◽  
pp. 2440-2450 ◽  
Author(s):  
Itaru Matsumura ◽  
Akira Kawasaki ◽  
Hirokazu Tanaka ◽  
Junko Sonoyama ◽  
Sachiko Ezoe ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Cell Lines ◽  
Direct Interaction ◽  
Myeloid Cell ◽  
Megakaryocytic Differentiation ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Endogenous Expression ◽  
Ras Activation

Abstract Lineage-specific transcription factors play crucial roles in the development of hematopoietic cells. In a previous study, it was demonstrated that Ras activation was involved in thrombopoietin-induced megakaryocytic differentiation. In this study, constitutive Ras activation by H-rasG12V evoked megakaryocytic maturation of erythroleukemia cell lines F-36P and K562, but not of myeloid cell line 32D cl3 that lacks GATA-1. However, the introduction of GATA-1 led to reprogramming of 32D cl3 toward erythrocytic/megakaryocytic lineage and enabled it to undergo megakaryocytic differentiation in response to H-rasG12V. In contrast, the overexpression of PU.1 and c-Myb changed the phenotype of K562 from erythroid to myeloid/monocytic lineage and rendered K562 to differentiate into granulocytes and macrophages in response to H-rasG12V, respectively. In GATA-1–transfected 32D cl3, the endogenous expression of PU.1 and c-Myb was easily detectable, but their activities were reduced severely. Endogenous GATA-1 activities were markedly suppressed in PU.1-transfected and c-myb–transfected K562. As for the mechanisms of these reciprocal inhibitions, GATA-1 and PU.1 were found to associate through their DNA-binding domains and to inhibit the respective DNA-binding activities of each other. In addition, c-Myb bound to GATA-1 and inhibited its DNA-binding activities. Mutant GATA-1 and PU.1 that retained their own transcriptional activities but could not inhibit the reciprocal partner were less effective in changing the lineage phenotype of 32D cl3 and K562. These results suggested that GATA-1 activities may be crucial for Ras-mediated megakaryocytic differentiation and that its activities may be regulated by the direct interaction with other lineage-specific transcription factors such as PU.1 and c-Myb.

scholarly journals Activated Notch Inhibits Myogenic Activity of the MADS-Box Transcription Factor Myocyte Enhancer Factor 2C

1999 ◽  
Vol 19 (4) ◽  
pp. 2853-2862 ◽  
Author(s):  
Jeanne Wilson-Rawls ◽  
Jeffery D. Molkentin ◽  
Brian L. Black ◽  
Eric N. Olson
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Notch Signaling Pathway ◽  
Mads Box ◽  
Dna Binding Domains ◽  
Muscle Gene Expression ◽  
Binding Domains ◽  
Myocyte Enhancer Factor ◽  
Bhlh Proteins ◽  
Enhancer Factor

ABSTRACT Skeletal muscle gene expression is dependent on combinatorial associations between members of the MyoD family of basic helix-loop-helix (bHLH) transcription factors and the myocyte enhancer factor 2 (MEF2) family of MADS-box transcription factors. The transmembrane receptor Notch interferes with the muscle-inducing activity of myogenic bHLH proteins, and it has been suggested that this inhibitory activity of Notch is directed at an essential cofactor that recognizes the DNA binding domains of the myogenic bHLH proteins. Given that MEF2 proteins interact with the DNA binding domains of myogenic bHLH factors to cooperatively regulate myogenesis, we investigated whether members of the MEF2 family might serve as targets for the inhibitory effects of Notch on myogenesis. We show that a constitutively activated form of Notch specifically blocks DNA binding by MEF2C, as well as its ability to cooperate with MyoD and myogenin to activate myogenesis. Responsiveness to Notch requires a 12-amino-acid region of MEF2C immediately adjacent to the DNA binding domain that is unique to this MEF2 isoform. Two-hybrid assays and coimmunoprecipitations show that this region of MEF2C interacts directly with the ankyrin repeat region of Notch. These findings reveal a novel mechanism for Notch-mediated inhibition of myogenesis and demonstrate that the Notch signaling pathway can discriminate between different members of the MEF2 family.

scholarly journals Structural Dynamics of the Heterodimerization Between the DNA-Binding Domains from Human FoxP1 and FoP2 Transcription Factors

2021 ◽  
Vol 120 (3) ◽  
pp. 127a
Author(s):  
Exequiel Medina ◽  
Ricardo Coñuecar ◽  
Cesar A. Ramirez-Sarmiento ◽  
Hugo Sanabria ◽  
Jorge Babul
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Structural Dynamics ◽  
Dna Binding Domains ◽  
Binding Domains
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