GA signalling and cross-talk with other signalling pathways

2015 ◽  
Vol 58 ◽  
pp. 49-60 ◽  
Author(s):  
Vai S. Lor ◽  
Neil E. Olszewski
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Growth And Development ◽  
Green Revolution ◽  
26S Proteasome ◽  
Signalling Pathways ◽  
Della Proteins ◽  
Expression Of Genes ◽  
Biosynthesis Gene ◽  
Ga Biosynthesis

Gibberellins (GAs) are phytohormones that regulate growth and development. DELLA proteins repress GA responses. GA binding to its receptor triggers a series of events that culminate in the destruction of DELLA proteins by the 26S proteasome, which removes the repression of GA signalling. DELLA proteins are transcription co-activators that induce the expression of genes which encode products that inhibit GA responses. In addition to repressing GA responses, DELLA proteins influence the activity of other signalling pathways and serve as a central hub from which other pathways influence GA signalling. In this role, DELLA proteins bind to and inhibit proteins, including transcription factors that act in the signalling pathways of other hormones and light. The binding of these proteins to DELLA proteins also inhibits DELLA activity. GA signalling is subject to homoeostatic regulation through GA-induced repression of GA biosynthesis gene expression, and increased production of the GA receptor and enzymes that catabolize bioactive GAs. This review also discusses the nature of mutant DELLA alleles that are used to produce high-yielding ‘Green Revolution’ cereal varieties, and highlights important gaps in our knowledge of GA signalling.

scholarly journals Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa

2018 ◽  
Vol 115 (48) ◽  
pp. E11321-E11330 ◽  
Author(s):  
Jie Hou ◽  
Xiaowen Shi ◽  
Chen Chen ◽  
Md. Soliman Islam ◽  
Adam F. Johnson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factors ◽  
Leaf Tissue ◽  
Global Gene Expression ◽  
Published Data ◽  
Chromosomal Imbalance ◽  
Regulatory Processes ◽  
Expression Of Genes ◽  
Global Impacts

Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.

scholarly journals Gene expression profiling of mantle cell lymphoma cells reveals aberrant expression of genes from the PI3K-AKT, WNT and TGFbeta signalling pathways

2005 ◽  
Vol 130 (4) ◽  
pp. 516-526 ◽  
Author(s):  
Edgar Gil Rizzatti ◽  
Roberto Passetto Falcao ◽  
Rodrigo Alexandre Panepucci ◽  
Rodrigo Proto-Siqueira ◽  
Wilma Terezinha Anselmo-Lima ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mantle Cell Lymphoma ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Cell Lymphoma ◽  
Signalling Pathways ◽  
Lymphoma Cells ◽  
Aberrant Expression ◽  
Expression Of Genes ◽  
Mantle Cell

scholarly journals DksA-dependent regulation of RpoS contributes to Borrelia burgdorferi tick-borne transmission and mammalian infectivity

2020 ◽  
Author(s):  
William K. Boyle ◽  
Crystal L. Richards ◽  
Daniel P. Dulebohn ◽  
Amanda K. Zalud ◽  
Jeff A. Shaw ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Lyme Disease ◽  
Borrelia Burgdorferi ◽  
Rna Polymerase ◽  
Nutrient Limitation ◽  
Expression Of Genes ◽  
Gene Regulatory ◽  
Transcription Assays

ABSTRACTThroughout its enzootic cycle, the Lyme disease spirochete Borreliella (Borrelia) burgdorferi, senses and responds to changes in its environment by using a small repertoire of transcription factors which coordinate the expression of genes required for infection of Ixodes ticks and various mammalian hosts. Among these transcription factors, the DnaK suppressor protein (DksA) plays a pivotal role in regulating gene expression in B. burgdorferi during periods of nutrient limitation and is required for mammalian infectivity. In many pathogenic bacteria, the gene regulatory activity of DksA along with the alarmone guanosine penta- and tetra-phosphate ((p)ppGpp) coordinates the stringent response to various environmental stresses including nutrient limitation. In this study, we sought to characterize the role of DksA in regulating the transcriptional activity of RNA polymerase and in the regulation of RpoS-dependent gene expression required for B. burgdorferi infectivity. Using in vitro transcription assays, we observed recombinant DksA inhibits RpoD-dependent transcription by B. burgdorferi RNA polymerase independent of ppGpp Additionally, we determined the pH-inducible expression of RpoS-dependent genes relies on DksA, but is independent of (p)ppGpp produced by Relbbu. Subsequent transcriptomic and western blot assays indicated DksA regulates the expression of BBD18, a protein previously implicated in the post-transcriptional regulation of RpoS. Moreover, we observed DksA was required for infection of mice following intraperitoneal inoculation or for transmission of B. burgdorferi by Ixodes scapularis nymphs. Together, these data suggest DksA plays a central role in coordinating transcriptional responses of B. burgdorferi required for infectivity through its interactions with RNA polymerase and post-transcriptional control of RpoS.Author SummaryLyme disease, caused by the spirochetal bacteria Borrelia burgdorferi, is the most common vector-borne illness in North America. The ability of B. burgdorferi to establish infection is predicated by its ability to coordinate the expression of virulence factors in response to diverse environmental stimuli encountered within Ixodes ticks and mammalian hosts. Previous studies have shown an essential role for the alternative sigma factor RpoS in regulating the expression of genes required for the successful transmission of B. burgdorferi by Ixodes ticks and infection of mammalian hosts. The DnaK suppressor protein (DksA) is a global gene regulator in B. burgdorferi that also contributes to the expression of RpoS-dependent genes. In this study, we determined DksA exerts its gene regulatory function through direct interactions with the B. burgdorferi RNA polymerase using in vitro transcription assays and controls the expression of RpoS-dependent genes required for mammalian infection by post-transcriptionally regulating cellular levels of RpoS. Our results demonstrate the utility of in vitro transcription assays to determine how gene regulatory proteins like DksA control gene expression in B. burgdorferi, and reveal a novel role for DksA in the infectious cycle of B. burgdorferi.

Gene Expression Profile in the CML Cell Line K562 Treated with SKI-606, a Dual Inhibitor of Src/Abl Kinase.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4870-4870
Author(s):  
Matteo Renzulli ◽  
Tiziana Grafone ◽  
Cristian Taccioli ◽  
Carolina Terragna ◽  
Frank Boschelli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Differential Expression ◽  
Signalling Pathways ◽  
Dual Inhibitor ◽  
Imatinib Resistance ◽  
Regulatory Pathways ◽  
Abl Kinase ◽  
Expression Of Genes ◽  
Wide Range

Abstract Although Imatinib represents the drug of choice for the treatment of Chronic Myeloid Leukemia (CML), new approaches to the treatment of CML remain a high priority in view of the continuing problems of Imatinib resistance. Previously (ASH 2004), we reported on the anti-proliferative and pro-apoptotic effects of the new drug, SKI-606, a potent Src/Abl kinase inhibitor, in blast crisis cell lines in vitro. Here we describe results of a transcriptional profiling study of SKI-606 activity in CML cells. Oligonucleotide microarray analysis using the Human 1A (V2) Oligo Microarrays of Agilent, containing more than 20,000 different genes was performed with untreated K562 cells and compared to the profile obtained from the same cells treated with 10 nM SKI-606 over a 48 h period. We labelled the amplified aRNA of the untreated cells with green (Cy3) dye and that of the treated with red (Cy5) dye, and also performed the reverse labeling experiment to confirm our data. Our approach to design comparisons utilizes a Lowess normalization and a filter followed by an analysis of variance (ANOVA) models to identify the genes with the greatest differential expression in the treated cells. We found identified 121 genes whose expression was modified by treatment with SKI-606. BCR-ABL activity results in activation of several downstream signalling pathways, including RAS/MAPK, PI3K/AKT and STAT pathways, which are implicated in mutagenic signalling and enhancement of survival. Our study showed that the expression of some genes involved in these regulatory pathways was altered by SKI-606. The greatest transcriptional changes (decreases or increases in gene expression of 2-fold or greater) were observed after 24h, while between 24 and 48h, the gene expression pattern stabilized. Ontological information concerning the cellular function of these transcripts suggests differential expression of genes associated with a wide range of cellular processes, including transcriptional regulation (CHAF1B, MRPL1, FLI1, FLN29 and CIR) and signal transduction (HRAS, ELMO, P114-RHO-GEF), among other functions. SKI-606 also modulates the expression of genes involved in cell cycle regulation such as MLLT7, a transcription factor that regulates the cell cycle through transcriptional activation of p27kip1. Our data also provide the first evidence that SKI-606 treatment is down-regulates apoptotic suppressor genes, such as LAMR1, RAC1 and DDB2. Interestingly, the component of the ubiquitin/proteasome pathway, FLJ12673, a subunit of the ubiquitin protein ligase complex, is downregulated by SKI-606 treatment. Currently, we are analyzing the most interesting modified genes to validate our data by Real Time PCR. Genome-wide expression-level analysis combined with biochemical studies of altered signalling pathways with cultured leukemia cells is expected to be a useful functional-genomic approach to more completely characterize the mechanism of action of this compound.

scholarly journals Regulation of Photomorphogenic Development by Plant Phytochromes

2019 ◽  
Vol 20 (24) ◽  
pp. 6165 ◽  
Author(s):  
Sharanya Tripathi ◽  
Quyen T. N. Hoang ◽  
Yun-Jeong Han ◽  
Jeong-Il Kim
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Life Cycle ◽  
Growth And Development ◽  
Developmental Stages ◽  
Red Light ◽  
Control Plant ◽  
Plant Growth And Development ◽  
Light Signals ◽  
Key Events

Photomorphogenesis and skotomorphogenesis are two key events that control plant development, from seed germination to flowering and senescence. A group of wavelength-specific photoreceptors, E3 ubiquitin ligases, and various transcription factors work together to regulate these two critical processes. Phytochromes are the main photoreceptors in plants for perceiving red/far-red light and transducing the light signals to downstream factors that regulate the gene expression network for photomorphogenic development. In this review, we highlight key developmental stages in the life cycle of plants and how phytochromes and other components in the phytochrome signaling pathway play roles in plant growth and development.

scholarly journals Gene Regulation via the Combination of Transcription Factors in the INDETERMINATE DOMAIN and GRAS Families

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 613
Author(s):  
Takuya Aoyanagi ◽  
Shun Ikeya ◽  
Atsushi Kobayashi ◽  
Akiko Kozaki
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Tissue Formation ◽  
Protein Protein Interactions ◽  
Short Root ◽  
Gras Family ◽  
Della Proteins ◽  
Culture Cells ◽  
Expression Of Genes ◽  
Dna Binding Properties

INDETERMINATE DOMAIN (IDD) family proteins are plant-specific transcription factors. Some Arabidopsis IDD (AtIDD) proteins regulate the expression of SCARECROW (SCR) by interacting with GRAS family transcription factors SHORT-ROOT (SHR) and SCR, which are involved in root tissue formation. Some AtIDD proteins regulate genes involved in the synthesis (GA3ox1) or signaling (SCL3) of gibberellic acid (GA) by interacting with DELLA proteins, a subfamily of the GRAS family. We analyzed the DNA binding properties and protein–protein interactions of select AtIDD proteins. We also investigated the transcriptional activity of the combination of AtIDD and GRAS proteins (AtIDD proteins combined with SHR and SCR or with REPRESSOR of ga1-3 (RGA)) on the promoters of SCR, SCL3, and GA3ox1 by conducting a transient assay using Arabidopsis culture cells. Our results showed that the SCR promoter could be activated by the IDD and RGA complexes and that the SCL3 and GA3ox1 promoters could be activated by the IDD, SHR, and SCR complexes, indicating the possibility that these complexes regulate and consequently coordinate the expression of genes involved in GA synthesis (GA3ox1), GA signaling (SCL3), and root formation (SCR).

scholarly journals Patterns of gene expression in the sheep heart during the perinatal period revealed by transcriptomic modeling

2015 ◽  
Vol 47 (9) ◽  
pp. 407-419 ◽  
Author(s):  
Elaine M. Richards ◽  
M. Belen Rabaglino ◽  
Andrew Antolic ◽  
Charles E. Wood ◽  
Maureen Keller-Wood
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Expression Patterns ◽  
Perinatal Period ◽  
Gene Expression Patterns ◽  
Acid Oxidation ◽  
Expression Of Genes ◽  
Development And Differentiation ◽  
Near Term ◽  
Coexpressed Genes

Septa from sheep hearts at 130 days gestation, term, and 14-day-old lambs were used to model the changes in gene expression patterns during the perinatal period using Agilent 15k ovine microarrays. We used Bioconductor for R to model five major patterns of coexpressed genes. Gene ontology and transcription factor analyses using Webgestalt modeled the biological significances and transcription factors of the gene expression patterns. Modeling indicated a decreased expression of genes associated with anatomical development and differentiation during this period, whereas those associated with increased protein synthesis and growth associated with maturation of the endoplasmic reticulum rose to term but did not further increase from the near term expression. Expression of genes associated with cell responsiveness, for example, immune responses, decreased at term but expression returned by postnatal day 14. Changes in genes related to metabolism showed differential substrate-associated patterns: those related to carbohydrate metabolism rose to term and remained stable thereafter, whereas those associated with fatty acid oxidation facility rose throughout the period. The timing of many of these maturational processes was earlier in relation to birth than in the rodent. The importance of the transcription factors, estrogen-related receptors, and v-myc avian myelocytomatosis viral oncogene homolog was also highlighted in the pattern of gene expression during development of the perinatal sheep heart.

scholarly journals pVHL regulates protein stability of TCF/LEF transcription factor family via ubiquitin-independent proteasomal degradation

2021 ◽  
Author(s):  
Caixia Wang ◽  
Xiaozhi Rong ◽  
Haifeng Zhang ◽  
Bo Wang ◽  
Yan Bai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Protein Stability ◽  
Ubiquitin Ligase ◽  
Target Gene ◽  
E3 Ubiquitin Ligase ◽  
Proteasomal Degradation ◽  
26S Proteasome ◽  
Cell Fate Decisions ◽  
Target Gene Expression

The Wnt/β-catenin signaling pathway plays key roles in development and adult tissue homeostasis by controlling cell proliferation and cell fate decisions. In this pathway, transcription factors TCF/LEFs are the key components to repress target gene expression by recruiting co-repressors or to activate target gene expression by recruiting β-catenin when the Wnt signals are absent or present, respectively. While progress has been made in our understanding of Wnt signaling regulation, the underlying mechanism that regulates the protein stability of the TCF/LEF family is far less clear. Here, we show that von Hippel-Lindau protein (pVHL), which is the substrate recognition component in an E3 ubiquitin ligase complex, controls TCF/LEF protein stability. Unexpectedly, pVHL directly binds to TCF/LEFs and promotes their proteasomal degradation independent of E3 ubiquitin ligase activity. Knockout of vhl in zebrafish embryos leads to a reduction of dorsal habenular neurons and this effect is upstream of dorsal habenular neurons phenotype in tcf7l2-null mutants. Our study uncovers a previously unknown mechanism for the protein stability regulation of the TCF/LEF transcription factors and demonstrates that pVHL contains a 26S proteasome binding domain that drives ubiquitin-independent proteasomal degradation. These findings provide new insights into the ubiquitin-independent actions of pVHL and uncover novel mechanistical regulation of Wnt/β-catenin signaling.

Regulation of gene expression in oncogenically transformed cells

1992 ◽  
Vol 70 (10-11) ◽  
pp. 980-997 ◽  
Author(s):  
Mohammed Dehbi ◽  
Pierre-André Bédard
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Transcriptional Activation ◽  
Cell Transformation ◽  
Regulation Of Gene Expression ◽  
Constitutive Expression ◽  
Transformed Cells ◽  
Extracellular Proteases ◽  
Expression Of Genes ◽  
Genes Encoding

Several genes expressed in response to growth factors are also regulated aberrantly in oncogenically transformed cells. The constitutive expression of genes encoding extracellular proteases, transcription factors, and cytokines is often correlated with cell transformation. In several instances, the uncontrolled expression of these genes is the result of transcriptional activation. Therefore, much attention has been devoted to the study of promoter function in transformed cells. We now review the results of recent investigations on transformation-dependent gene expression. The activation of several transcription factors in oncogenically- transformed cells is described. Results regarding the regulation of promoters through PRD II/κB are presented for cells transformed by a variety of oncogenes. Finally, we discuss the significance of transcription factor activation in the process of cell transformation.Key words: oncogenes, transcription factors, transformation, pp60v-src.

scholarly journals Exogenous Gene Expression and Insect Resistance in Dual Bt Toxin Populus × euramericana ‘Neva’ Transgenic Plants

2021 ◽  
Vol 12 ◽  
Author(s):  
Yachao Ren ◽  
Xinglu Zhou ◽  
Yan Dong ◽  
Jun Zhang ◽  
Jinmao Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Insect Resistance ◽  
Growth And Development ◽  
Hyphantria Cunea ◽  
Bt Toxin ◽  
Toxin Genes ◽  
Feeding Experiments ◽  
Expression Of Genes ◽  
Transgenic Lines ◽  
Exogenous Gene

Bacillus thuringiensis (Bt) insecticidal protein genes are important tools in efforts to develop insect resistance in poplar. In this study, the Cry1Ac and Cry3A Bt toxin genes were simultaneously transformed into the poplar variety Populus × euramericana ‘Neva’ by Agrobacterium-mediated transformation to explore the exogenous gene expression and insect resistance, and to examine the effects of Bt toxin on the growth and development of Anoplophora glabripennis larvae after feeding on the transgenic plant. Integration and expression of the transgenes were determined by molecular analyses and the insect resistance of transgenic lines was evaluated in feeding experiments. Sixteen transgenic dual Bt toxin genes Populus × euramericana ‘Neva’ lines were obtained. The dual Bt toxin genes were expressed at both the transcriptional and translational levels; however, Cry3A protein levels were much higher than those of Cry1Ac. Some of the transgenic lines exhibited high resistance to the first instar larvae of Hyphantria cunea and Micromelalopha troglodyta, and the first and second instar larvae and adults of Plagiodera versicolora. Six transgenic lines inhibited the growth and development of A. glabripennis larvae. The differences in the transcriptomes of A. glabripennis larvae fed transgenic lines or non-transgenic control by RNA-seq analyses were determined to reveal the mechanism by which Bt toxin regulates the growth and development of longicorn beetle larvae. The expression of genes related to Bt prototoxin activation, digestive enzymes, binding receptors, and detoxification and protective enzymes showed significant changes in A. glabripennis larvae fed Bt toxin, indicating that the larvae responded by regulating the expression of genes related to their growth and development. This study lay a theoretical foundation for developing resistance to A. glabripennis in poplar, and provide a foundation for exploring the mechanism of Bt toxin action on Cerambycidae insects.

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