scholarly journals Synergistic binding of bHLH transcription factors to the promoter of the maize NADP-ME gene used in C4 photosynthesis is based on an ancient code found in the ancestral C3 state

2018 ◽  
Author(s):  
Ana Rita Borba ◽  
Tânia S. Serra ◽  
Alicja Górska ◽  
Paulo Gouveia ◽  
André M. Cordeiro ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Mobility Shift ◽  
Helix Loop Helix ◽  
Specific Accumulation ◽  
Cell Type Specific ◽  
Bhlh Transcription Factors ◽  
Electrophoretic Mobility Shift Assays ◽  
Element Pair

AbstractC4 photosynthesis has evolved repeatedly from the ancestral C3 state to generate a carbon concentrating mechanism that increases photosynthetic efficiency. This specialised form of photosynthesis is particularly common in the PACMAD clade of grasses, and is used by many of the world’s most productive crops. The C4 cycle is accomplished through cell-type specific accumulation of enzymes but cis-elements and transcription factors controlling C4 photosynthesis remain largely unknown. Using the NADP-Malic Enzyme (NADP-ME) gene as a model we aimed to better understand molecular mechanisms associated with the evolution of C4 photosynthesis. Two basic Helix-Loop-Helix (bHLH) transcription factors, ZmbHLH128 and ZmbHLH129, were shown to bind the C4NADP-ME promoter from maize. These proteins form heterodimers and ZmbHLH129 impairs trans-activation by ZmbHLH128. Electrophoretic mobility shift assays indicate that a pair of cis-elements separated by a seven base pair spacer synergistically bind either ZmbHLH128 or ZmbHLH129. This pair of cis-elements is found in both C3 and C4 species of the PACMAD clade. Our analysis is consistent with this cis-element pair originating from a single motif present in the ancestral C3 state. We conclude that C4 photosynthesis has co-opted an ancient C3 regulatory code built on G-box recognition by bHLH to regulate the NADP-ME gene. More broadly, our findings also contribute to the understanding of gene regulatory networks controlling C4 photosynthesis.

scholarly journals Atoh8 in Development and Disease

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 136
Author(s):  
Satya Srirama Karthik Divvela ◽  
Darius Saberi ◽  
Beate Brand-Saberi
Keyword(s):  
Transcription Factors ◽  
Embryonic Development ◽  
Subcellular Location ◽  
Transcriptional Regulators ◽  
Special Group ◽  
Helix Loop Helix ◽  
Wide Range ◽  
Disease Initiation ◽  
Bhlh Transcription Factors ◽  
Bhlh Proteins

Atoh8 belongs to a large superfamily of transcriptional regulators called basic helix-loop-helix (bHLH) proteins. bHLH proteins have been identified in a wide range of organisms from yeast to humans. The members of this special group of transcription factors were found to be involved not only in embryonic development but also in disease initiation and its progression. Given their importance in several fundamental processes, the translation, subcellular location and turnover of bHLH proteins is tightly regulated. Alterations in the expression of bHLH proteins have been associated with multiple diseases also in context with Atoh8 which seems to unfold its functions as both transcriptional activator and repressor. Like many other bHLH transcription factors, so far, Atoh8 has also been observed to be involved in both embryonic development and carcinogenesis where it mainly acts as tumor suppressor. This review summarizes our current understanding of Atoh8 structure, function and regulation and its complex and partially controversial involvement in development and disease.

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.

scholarly journals Molecular Logic of Hypothalamus Development

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A507-A507
Author(s):  
Thomas Kim
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Time ◽  
Specific Gene ◽  
Molecular Logic ◽  
Hypothalamic Nuclei ◽  
Physiological Homeostasis ◽  
Mutant Lines

Abstract The hypothalamus is a central regulator of physiological homeostasis. During development, multiple transcription factors coordinate the patterning and specification of hypothalamic nuclei. However, the molecular mechanisms controlling hypothalamic patterning and cell fate specification are poorly understood. To identify genes that control these processes, we have previously used single-cell RNA sequencing (scRNA-Seq) to profile mouse hypothalamic gene expression across multiple developmental time points and established database HyDD (Hypothalamus Developmental Database). We next used HyDD to characterize multiple mutant lines targetting key transcription factors that came out from our scRNA-Seq database (Nkx2.2, Dlx1/2, Isl1, Foxd1, Lhx2), and was able to comprehensively characterize mutants that have altered hypothalamic patterning. Our phenotype result supports a modified columnar model of organization for the diencephalon, where prethalamus and hypothalamus are situated in adjacent dorsal and ventral domains of the anterior diencephalon. Furthermore, using our mouse hypothalamus as a guideline, we are comparing scRNA-Seq dataset of developing chicken, zebrafish and human hypothalamus, to identify evolutionarily conserved and divergent region-specific gene regulatory networks. Lastly, we are improving mouse HyDD, in order to characterize adult hypothalamus neuronal subtypes.

scholarly journals Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum.

2020 ◽  
Author(s):  
Javier Canales ◽  
Felipe Uribe ◽  
Carlos Henríquez-Valencia ◽  
Carlos Lovazzano ◽  
Joaquín Medina ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Essential Element ◽  
Transcript Level ◽  
Central Component ◽  
Transcriptomic Response ◽  
Starvation Response ◽  
Expression Of Genes ◽  
The Impact

Abstract Background: Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in Arabidopsis thaliana and a limited number of crop plants. However, we still lack a thorough understanding of the molecular mechanisms and regulatory networks underlying sulfate deficiency in most plants. In this work we analyzed the impact of sulfate starvation on the transcriptome of tomato plants to identify regulatory networks and key transcriptional regulators at a temporal and organ scale. Results: Sulfate starvation reduces the growth of roots and leaves which is accompanied by major changes in the organ transcriptome, with the response being temporally earlier in roots than leaves. Comparative analysis showed that a major part of the Arabidopsis and tomato transcriptomic response to sulfate starvation is conserved between these plants and allowed for the identification of processes specifically regulated in tomato at the transcript level, including the control of internal phosphate levels. Integrative gene network analysis uncovered key transcription factors controlling the temporal expression of genes involved in sulfate assimilation, as well as cell cycle, cell division and photosynthesis during sulfate starvation in tomato roots and leaves. Interestingly, one of these transcription factors presents a high identity with SULFUR LIMITATION1, a central component of the sulfate starvation response in Arabidopsis. Conclusions: Together, our results provide the first comprehensive catalog of sulfate-responsive genes in tomato, as well as novel regulatory targets for future functional analyses in tomato and other crops.

scholarly journals Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in Caenorhabditis elegans

Development ◽  
2021 ◽  
Vol 148 (11) ◽  
Author(s):  
Neda Masoudi ◽  
Eviatar Yemini ◽  
Ralf Schnabel ◽  
Oliver Hobert
Keyword(s):  
Transcription Factors ◽  
Caenorhabditis Elegans ◽  
Contralateral Side ◽  
Mirror Image ◽  
Neuronal Markers ◽  
C Elegans ◽  
Helix Loop Helix ◽  
Distinct Lineage ◽  
Bhlh Transcription Factors ◽  
Identity Transformations

ABSTRACT Cells of the same type can be generated by distinct cellular lineages that originate in different parts of the developing embryo (‘lineage convergence’). Several Caenorhabditis elegans neuron classes composed of left/right or radially symmetric class members display such lineage convergence. We show here that the C. elegans Atonal homolog lin-32 is differentially expressed in neuronal lineages that give rise to left/right or radially symmetric class members. Loss of lin-32 results in the selective loss of the expression of pan-neuronal markers and terminal selector-type transcription factors that confer neuron class-specific features. Another basic helix-loop-helix (bHLH) gene, the Achaete-Scute homolog hlh-14, is expressed in a mirror image pattern relative to lin-32 and is required to induce neuronal identity and terminal selector expression on the contralateral side of the animal. These findings demonstrate that distinct lineage histories converge via different bHLH factors at the level of induction of terminal selector identity determinants, which thus serve as integrators of distinct lineage histories. We also describe neuron-to-neuron identity transformations in lin-32 mutants, which we propose to also be the result of misregulation of terminal selector gene expression.

scholarly journals Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce

2020 ◽  
Vol 117 (52) ◽  
pp. 33668-33678
Author(s):  
Changchun Yu ◽  
Chenghuan Yan ◽  
Yuling Liu ◽  
Yali Liu ◽  
Yue Jia ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Vegetable Crops ◽  
Mobility Shift ◽  
Unique Type ◽  
Chip Sequencing ◽  
Head Development ◽  
Enhanced Expression ◽  
Trait Locus ◽  
Leafy Head ◽  
Electrophoretic Mobility Shift Assays

Leafy head is a unique type of plant architecture found in some vegetable crops, with leaves bending inward to form a compact head. The genetic and molecular mechanisms underlying leafy head in vegetables remain poorly understood. We genetically fine-mapped and cloned a major quantitative trait locus controlling heading in lettuce. The candidate gene (LsKN1) is a homolog of knotted 1 (KN1) from Zea mays. Complementation and CRISPR/Cas9 knockout experiments confirmed the role of LsKN1 in heading. In heading lettuce, there is a CACTA-like transposon inserted into the first exon of LsKN1 (LsKN1▽). The transposon sequences act as a promoter rather than an enhancer and drive high expression of LsKN1▽. The enhanced expression of LsKN1▽ is necessary but not sufficient for heading in lettuce. Data from ChIP-sequencing, electrophoretic mobility shift assays, and dual luciferase assays indicate that the LsKN1▽ protein binds the promoter of LsAS1 and down-regulates its expression to alter leaf dorsoventrality. This study provides insight into plant leaf development and will be useful for studies on heading in other vegetable crops.

Transcriptional Regulation of Hepcidin by Iron.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2664-2664
Author(s):  
Pauline Lee ◽  
Truksa Jaroslav ◽  
Hongfan Peng ◽  
Ernest Beutler
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Iron Homeostasis ◽  
Mobility Shift ◽  
Consensus Sequences ◽  
High Iron ◽  
Amino Acid Peptide ◽  
Nuclear Extracts ◽  
Iron Deficient ◽  
Electrophoretic Mobility Shift Assays

Abstract Transcriptional regulation by iron in mammalian systems is poorly understood. Hepcidin, a 25 amino acid peptide that plays a central role in iron homeostasis, is transcriptionally regulated by iron. A region of the murine hepcidin promoter 1.6 to 1.8 kb upstream from the start of translation was recently identified to be important in transcriptional regulation by iron (Truksa J, et al. The distal location of the iron responsive region of the hepcidin promoter. Blood DOI 10.1182/blood-2007-05-091108, 2007). In order to identify transcription factors that might be important in regulation by iron, transcription factor microarray analyses (Panomics TranSignal Protein/DNA Array) were performed with nuclear extracts from livers of mice made iron deficient or iron loaded for 4 weeks. The analyses revealed 43 transcription factors that were upregulated in iron loaded liver nuclear extracts and 39 transcription factors that were upregulated in iron deficient nuclear extracts. In the region of the promoter we had found essential for transcriptional regulation by iron, −1.6 to −1.8 kb, consensus motifs were identified by Genomatix MatInspector for 10 transcription factors that corresponded to transcription factors upregulated in high iron nuclear extracts by array analyses. Similarly, the consensus sequences for 5 transcription factors corresponded to transcription factors identified in iron deficient nuclear extracts. Electrophoretic mobility shift assays were performed with probes across this region of the murine hepcidin promoter. Several probes exhibited differential binding between deficient and high iron nuclear extracts. These include the probe encompassing the CCAAT box and MEL1 motif, a probe containing a HLH motif, and a probe containing a bZIP and COUP motif. The probe containing the CCAAT motif was supershifted with antibodies against CBF, but was not supershifted with antibodies against SMAD4, CEBPα, and COUP. The probe containing a bZIP and COUP motif can be supershifted with antibodies against COUP-Tf and HNF4α, but not with antibodies against SMAD4, CEBPα, and COUP. Our data suggest that CBFA, COUP, and HNF4α are involved in transcriptional regulation of hepcidin by iron.

scholarly journals Specific Protein-Protein Interaction between Basic Helix-Loop-Helix Transcription Factors and Homeoproteins of the Pitx Family

2000 ◽  
Vol 20 (13) ◽  
pp. 4826-4837 ◽  
Author(s):  
Gino Poulin ◽  
Mélanie Lebel ◽  
Michel Chamberland ◽  
Francois W. Paradis ◽  
Jacques Drouin
Keyword(s):  
Transcription Factors ◽  
Critical Role ◽  
Specific Protein ◽  
Physical Interaction ◽  
Protein Protein Interaction ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Factors ◽  
Pomc Gene ◽  
Bhlh Transcription Factors

ABSTRACT Homeoproteins and basic helix-loop-helix (bHLH) transcription factors are known for their critical role in development and cellular differentiation. The pituitary pro-opiomelanocortin (POMC) gene is a target for factors of both families. Indeed, pituitary-specific transcription of POMC depends on the action of the homeodomain-containing transcription factor Pitx1 and of bHLH heterodimers containing NeuroD1. We now show lineage-restricted expression of NeuroD1 in pituitary corticotroph cells and a direct physical interaction between bHLH heterodimers and Pitx1 that results in transcriptional synergism. The interaction between the bHLH and homeodomains is restricted to ubiquitous (class A) bHLH and to the Pitx subfamily. Since bHLH heterodimers interact with Pitx factors through their ubiquitous moiety, this mechanism may be implicated in other developmental processes involving bHLH factors, such as neurogenesis and myogenesis.

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