scholarly journals Developmental regulators FlbE/D orchestrate the polarity site-to-nucleus dynamics of the fungal bZIP FlbB

2018 ◽  
Author(s):  
Ainara Otamendi ◽  
Elixabet Perez-de-Nanclares-Arregi ◽  
Elixabet Oiartzabal ◽  
Marc S. Cortese ◽  
Eduardo A. Espeso ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Aspergillus Nidulans ◽  
Nuclear Accumulation ◽  
Long Distance ◽  
Developmental Transitions ◽  
Viral Peptide ◽  
Lxxll Motif ◽  
Polarized Cells ◽  
Transduction Mechanisms

AbstractPermanently polarized cells have developed transduction mechanisms linking polarity-sites with gene regulation in the nucleus. In neurons, one mechanism is based on long-distance retrograde migration of transcription factors (TFs).Aspergillus nidulansFlbB is the only known fungal TF shown to migrate retrogradely to nuclei from the polarized region of fungal cells known as hyphae. There, FlbB controls developmental transitions by triggering the production of asexual multicellular structures. FlbB dynamics in hyphae is orchestrated by regulators FlbE and FlbD. At least three FlbE domains are involved in the acropetal transport of FlbB, with a final MyoE/actin filament-dependent step from the subapex to the apex. Experiments employing a T2A viral peptide-containing chimera (FlbE::mRFP::T2A::FlbB::GFP) suggest that apical FlbB/FlbE interaction is inhibited in order to initiate a dynein-dependent FlbB transport to nuclei. FlbD controls the nuclear accumulation of FlbB through a cMyb domain and a C-terminal LxxLL motif. Overall, results elucidate a highly dynamic pattern of FlbB interactions, which enable timely developmental induction. Furthermore, this system establishes a reference for TF-based long-distance signaling in permanently polarized cells.

scholarly journals MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development

2021 ◽  
Vol 22 (7) ◽  
pp. 3560
Author(s):  
Ruixue Xiao ◽  
Chong Zhang ◽  
Xiaorui Guo ◽  
Hui Li ◽  
Hai Lu
Keyword(s):  
Cell Wall ◽  
Transcription Factors ◽  
Secondary Wall ◽  
Secondary Cell Wall ◽  
Lignin Biosynthesis ◽  
Cell Wall Formation ◽  
Long Distance ◽  
Secondary Cell Wall Formation ◽  
Myb Transcription Factors ◽  
Wall Formation

The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.

scholarly journals HbxB Is a Key Regulator for Stress Response and β-Glucan Biogenesis in Aspergillus nidulans

2021 ◽  
Vol 9 (1) ◽  
pp. 144
Author(s):  
Sung-Hun Son ◽  
Mi-Kyung Lee ◽  
Ye-Eun Son ◽  
Hee-Soo Park
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Aspergillus Nidulans ◽  
Deletion Mutant ◽  
Phenotypic Analysis ◽  
Spore Viability ◽  
Fungal Development ◽  
Expression Of Genes ◽  
Trehalose Biosynthesis

Homeobox transcription factors are conserved in eukaryotes and act as multi-functional transcription factors in filamentous fungi. Previously, it was demonstrated that HbxB governs fungal development and spore viability in Aspergillus nidulans. Here, the role of HbxB in A. nidulans was further characterized. RNA-sequencing revealed that HbxB affects the transcriptomic levels of genes associated with trehalose biosynthesis and response to thermal, oxidative, and radiation stresses in asexual spores called conidia. A phenotypic analysis found that hbxB deletion mutant conidia were more sensitive to ultraviolet stress. The loss of hbxB increased the mRNA expression of genes associated with β-glucan degradation and decreased the amount of β-glucan in conidia. In addition, hbxB deletion affected the expression of the sterigmatocystin gene cluster and the amount of sterigmatocystin. Overall, these results indicated that HbxB is a key transcription factor regulating trehalose biosynthesis, stress tolerance, β-glucan degradation, and sterigmatocystin production in A.nidulans conidia.

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 Regulation of rice root development by a retrotransposon acting as a microRNA sponge

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Jungnam Cho ◽  
Jerzy Paszkowski
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Root Development ◽  
Binding Sites ◽  
Transcriptional Control ◽  
Specific Expression ◽  
Ability To Act ◽  
Specific Accumulation ◽  
In Trans ◽  
Microrna Sponge

It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.

scholarly journals Transcriptomic, Protein-DNA Interaction, and Metabolomic Studies of VosA, VelB, and WetA in Aspergillus nidulans Asexual Spores

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ming-Yueh Wu ◽  
Matthew E. Mead ◽  
Mi-Kyung Lee ◽  
George F. Neuhaus ◽  
Donovon A. Adpressa ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Secondary Metabolism ◽  
Aspergillus Nidulans ◽  
Filamentous Fungi ◽  
Genetic Regulatory Networks ◽  
Asexual Development ◽  
Morphological Development ◽  
Vast Number ◽  
Content Type ◽  
Metabolic Remodeling

ABSTRACT In filamentous fungi, asexual development involves cellular differentiation and metabolic remodeling leading to the formation of intact asexual spores. The development of asexual spores (conidia) in Aspergillus is precisely coordinated by multiple transcription factors (TFs), including VosA, VelB, and WetA. Notably, these three TFs are essential for the structural and metabolic integrity, i.e., proper maturation, of conidia in the model fungus Aspergillus nidulans. To gain mechanistic insight into the complex regulatory and interdependent roles of these TFs in asexual sporogenesis, we carried out multi-omics studies on the transcriptome, protein-DNA interactions, and primary and secondary metabolism employing A. nidulans conidia. RNA sequencing and chromatin immunoprecipitation sequencing analyses have revealed that the three TFs directly or indirectly regulate the expression of genes associated with heterotrimeric G-protein signal transduction, mitogen-activated protein (MAP) kinases, spore wall formation and structural integrity, asexual development, and primary/secondary metabolism. In addition, metabolomics analyses of wild-type and individual mutant conidia indicate that these three TFs regulate a diverse array of primary metabolites, including those in the tricarboxylic acid (TCA) cycle, certain amino acids, and trehalose, and secondary metabolites such as sterigmatocystin, emericellamide, austinol, and dehydroaustinol. In summary, WetA, VosA, and VelB play interdependent, overlapping, and distinct roles in governing morphological development and primary/secondary metabolic remodeling in Aspergillus conidia, leading to the production of vital conidia suitable for fungal proliferation and dissemination. IMPORTANCE Filamentous fungi produce a vast number of asexual spores that act as efficient propagules. Due to their infectious and/or allergenic nature, fungal spores affect our daily life. Aspergillus species produce asexual spores called conidia; their formation involves morphological development and metabolic changes, and the associated regulatory systems are coordinated by multiple transcription factors (TFs). To understand the underlying global regulatory programs and cellular outcomes associated with conidium formation, genomic and metabolomic analyses were performed in the model fungus Aspergillus nidulans. Our results show that the fungus-specific WetA/VosA/VelB TFs govern the coordination of morphological and chemical developments during sporogenesis. The results of this study provide insights into the interdependent, overlapping, or distinct genetic regulatory networks necessary to produce intact asexual spores. The findings are relevant for other Aspergillus species such as the major human pathogen Aspergillus fumigatus and the aflatoxin producer Aspergillus flavus.

scholarly journals Targeted Next Generation Sequencing Reveals a Third Breakpoint Cluster Region and New Partner Genes in the KMT2A Recombinome

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 3327-3327
Author(s):  
Claus Meyer ◽  
Patrizia Larghero ◽  
Bruno Lopes ◽  
Aurélie Caye-Eude ◽  
Hélène Cavé ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Multiplex Pcr ◽  
Conflicts Of Interest ◽  
Future Research ◽  
Striking Difference ◽  
Elongation Complex ◽  
Long Distance ◽  
Acute Leukemias ◽  
Breakpoint Cluster Region ◽  
Cluster Region

Abstract Chromosomal rearrangements of the KMT2A gene are associated with acute leukemias and myelodysplastic syndromes. The large number of known KMT2A fusions (>100) renders a precise diagnosis a demanding task. More than 50% of all KMT2A partner genes have been analyzed at the DCAL, including the novel partner genes BCAS4, FAM13A, RANBP3, and STK4. Even though all KMT2A rearrangements are associated with high-risk acute leukemia, the outcome (poor or very poor) is influenced by the partner gene. So far, we have analyzed more than 3,200 patients positive for a KMT2A rearrangement. The breakpoints of these cases are located mainly in the major breakpoint cluster region (bcr1) and to a small extent in the recently described minor bcr (bcr2). A small number of breakpoints were also found outside of these two bcrs. Most of these patients were analyzed by long distance inverse (LDI)- or multiplex-PCR which only cover bcr1. More recently, we used targeted KMT2A-NGS with whole gene coverage in over 450 patients, which was initially applied selectively in patients negative by LDI- and multiplex-PCR and then used more widely. Within the KMT2A-NGS group, 410 patients had bcr1 breakpoints mainly between the KMT2A exons 7 and 13, while 46 patients bcr2 breakpoints mainly between exons 20 and 24. Of note, five patients had their breakpoint outside of these two bcrs: three of them within intron 2 and no functional KMT2A rearrangement; the other two within intron 35 and intron 36, fusing almost the whole KMT2A gene in frame to the respective partner genes ARHGEF12 and MLLT4. These two breakpoints may define a third and rare bcr (bcr3), although further cases are needed to support this hypothesis. Interestingly, 70 patients displayed a 3'-KMT2A deletion, indicating that the number of terminal deletions is higher than described previously. Two patients had a 5'-KMT2A deletion. All deletions started or ended in bcr1 and bcr2. We also observed a striking difference in the distribution of partner genes between bcr1 and bcr2. The most frequent translocation partners fused to bcr1 sites are transcription factors, while the partner genes linked to bcr2 sites generally code for cytosolic proteins. In bcr1, the 4 most frequent partner genes AFF1, MLLT3, MLLT1, and MLLT10, found in 80% of cases, all code for transcription factors that are part of the super elongation complex (SEC). These fusions therefore all lead to disruption of the hematopoietic lineage commitment. In contrast in bcr2, 3 partner genes USP2, MLLT4, and USP8 account for 85% of the cases. USP2 and USP8 are ubiquitin specific peptidases involved in cell signaling and exclusively fused to bcr2 in KMT2A. While MLLT4 is found as a partner in bcr1, bcr2 and bcr3 fusions; unlike other recurrent KMT2A partners linked to bcr1, it is not a transcription factor and it exerts oncogenic potential via dimerization like other cytosolic partners. We hypothesize that the oncogenic properties of USP2 and USP8 are dependent on dimerization like MLLT4 and that the most frequent fusions involving at different bcrs favor different oncogenic mechanisms: bcr1 transactivation and bcr2 dimerization. Further studies are needed to explain why USP2 and USP8 are exclusively associated with bcr2, and why the most frequent partner genes AFF1 and MLLT3 of the bcr1 are less frequent in bcr2. In conclusion, targeted NGS combined with bioinformatic analysis has expanded our knowledge of the KMT2A recombinome to include more fusion partners and has generated new hypotheses for future research on oncogenic mechanisms. Disclosures No relevant conflicts of interest to declare.

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.

Transvection and long-distance gene regulation

BioEssays ◽  
1990 ◽  
Vol 12 (9) ◽  
pp. 409-414 ◽  
Author(s):  
Vincenzo Pirrotta
Keyword(s):  
Gene Regulation ◽  
Long Distance

scholarly journals FoxO1 and FoxM1 Transcription Factors Have Antagonistic Functions in Neonatal Cardiomyocyte Cell-Cycle Withdrawal and IGF1 Gene Regulation

2013 ◽  
Vol 112 (2) ◽  
pp. 267-277 ◽  
Author(s):  
Arunima Sengupta ◽  
Vladimir V. Kalinichenko ◽  
Katherine E. Yutzey
Keyword(s):  
Cell Cycle ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Neonatal Cardiomyocyte
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