Transcriptional responses to low temperature and their regulation in Arabidopsis

2003 ◽  
Vol 81 (12) ◽  
pp. 1168-1174 ◽  
Author(s):  
Tong Zhu ◽  
Nicholas J Provart
Keyword(s):  
Low Temperature ◽  
Signaling Pathways ◽  
Low Temperatures ◽  
Quantitative Difference ◽  
Transcriptional Response ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Mrna Levels ◽  
Transcriptional Responses ◽  
Cold Response

Recent studies have used a transcriptional profiling approach to identify genes in Arabidopsis that respond at the level of transcript abundance to cold (4 °C) or chilling (13 °C) temperatures. Results have shown that plants respond to low temperatures by altering mRNA levels of a large number of genes belonging to different independent pathways. Early transcriptional response to low temperatures frequently involves signaling pathways used to respond to other environmental stresses, indicating the existence and involvement of a complex genetic network. Genes with functions specific to low-temperature signaling pathways, and those with functions in multiple signaling pathways, especially those encoding transcription factors and other signaling molecules, have been identified based on their transcriptional responses to different environmental stresses. The qualitative and quantitative difference in transcriptional response to chilling and cold suggests that plants might have different molecular mechanisms to acclimate to different types of low-temperature stresses. The regulation and interactions of genes involved in low-temperature response at the transcriptional level has been further explored by computational methods, and preliminary results have identified motifs that are known to be important for cold response, raising the possibility of a better understanding of the processes involved.Key words: Arabidopsis, low-temperature stress, gene expression, transcriptional regulation, microarray.

scholarly journals Estrogen Opposes the Apoptotic Effects of Bone Morphogenetic Protein 7 on Tissue Remodeling

2000 ◽  
Vol 20 (13) ◽  
pp. 4626-4634 ◽  
Author(s):  
David G. Monroe ◽  
Donald F. Jin ◽  
Michel M. Sanders
Keyword(s):  
Gene Expression ◽  
Growth Factor ◽  
Signaling Pathways ◽  
Bone Morphogenetic Protein ◽  
Transcriptional Level ◽  
Mrna Levels ◽  
Bone Morphogenetic Protein 7 ◽  
Reproductive Tissues ◽  
Morphogenetic Protein ◽  
Estrogen Withdrawal

ABSTRACT Interactions between estrogen and growth factor signaling pathways at the level of gene expression play important roles in the function of reproductive tissues. For example, estrogen regulates transforming growth factor beta (TGFβ) in the uterus during the proliferative phase of the mammalian reproductive cycle. Bone morphogenetic protein 7 (BMP-7), a member of the TGFβ superfamily, is also involved in the development and function of reproductive tissues. However, relatively few studies have addressed the expression of BMP-7 in reproductive tissues, and the role of BMP-7 remains unclear. As part of an ongoing effort to understand how estrogen represses gene expression and to study its interactions with other signaling pathways, chick BMP-7 (cBMP-7) was cloned. cBMP-7 mRNA levels are repressed threefold within 8 h following estrogen treatment in the chick oviduct, an extremely estrogen-responsive reproductive tissue. This regulation occurs at the transcriptional level. Estrogen has a protective role in many tissues, and withdrawal from estrogen often leads to tissue regression; however, the mechanisms mediating regression of the oviduct remain unknown. Terminal transferase-mediated end-labeling and DNA laddering assays demonstrated that regression of the oviduct during estrogen withdrawal involves apoptosis, which is a novel observation. cBMP-7 mRNA levels during estrogen withdrawal increase concurrently with the apoptotic index of the oviduct. Furthermore, addition of purified BMP-7 induces apoptosis in primary oviduct cells. This report demonstrates that the function of BMP-7 in the oviduct involves the induction of apoptosis and that estrogen plays an important role in opposing this function.

scholarly journals Role of Calcium Signaling in the Transcriptional Regulation of the Apicoplast Genome ofPlasmodium falciparum

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Sabna Cheemadan ◽  
Ramya Ramadoss ◽  
Zbynek Bozdech
Keyword(s):  
Calcium Binding ◽  
Transcriptional Response ◽  
Mrna Levels ◽  
Transcriptional Responses ◽  
Calcium Dependent ◽  
Regulatory Processes ◽  
Ofplasmodium Falciparum ◽  
Ef Hand ◽  
Apicoplast Genome

Calcium is a universal second messenger that plays an important role in regulatory processes in eukaryotic cells. To understand calcium-dependent signaling in malaria parasites, we analyzed transcriptional responses ofPlasmodium falciparumto two calcium ionophores (A23187 and ionomycin) that cause redistribution of intracellular calcium within the cytoplasm. While ionomycin induced a specific transcriptional response defined by up- or downregulation of a narrow set of genes, A23187 caused a developmental arrest in the schizont stage. In addition, we observed a dramatic decrease of mRNA levels of the transcripts encoded by the apicoplast genome during the exposure ofP. falciparumto both calcium ionophores. Neither of the ionophores caused any disruptions to the DNA replication or the overall apicoplast morphology. This suggests that the mRNA downregulation reflects direct inhibition of the apicoplast gene transcription. Next, we identify a nuclear encoded protein with a calcium binding domain (EF-hand) that is localized to the apicoplast. Overexpression of this protein (termed PfACBP1) inP. falciparumcells mediates an increased resistance to the ionophores which suggests its role in calcium-dependent signaling within the apicoplast. Our data indicate that theP. falciparumapicoplast requires calcium-dependent signaling that involves a novel protein PfACBP1.

scholarly journals Genomic insights into temperature-dependent transcriptional responses ofKosmotoga olearia, a deep-biosphere bacterium that can grow from 20°C to 79°C

2016 ◽  
Author(s):  
Stephen M. J. Pollo ◽  
Abigail A. Adebusuyi ◽  
Timothy J. Straub ◽  
Julia M. Foght ◽  
Olga Zhaxybayeva ◽  
...  
Keyword(s):  
Ribosomal Proteins ◽  
Transcriptional Response ◽  
Genomic Analysis ◽  
Cellular Membrane ◽  
Comparative Genomic ◽  
Deep Biosphere ◽  
Transcriptional Responses ◽  
Cold Response ◽  
Temperature Growth ◽  
Temperature Range

AbstractTemperature is one of the defining parameters of an ecological niche. Most organisms thrive within a temperature range that rarely exceeds ∼ 30°C, but the deep subsurface bacteriumKosmotoga oleariacan grow over a temperature range of 59°C (20°C -79°C). To identify genes correlated with this flexible phenotype, we compared transcriptomes ofK. oleariacultures grown at its optimal 65°C to those at 30°C, 40°C, and 77°C. The temperature treatments affected expression of 573 of 2,224K. oleariagenes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures and up-regulation of amino acid metabolism at lower temperatures. At sub-optimal temperatures, many transcriptional changes were similar to those observed in mesophilic bacteria at physiologically low temperatures, including up-regulation of typical cold stress genes and ribosomal proteins. Comparative genomic analysis of additional Thermotogae genomes, indicate that one ofK. olearia's strategies for low temperature growth is increased copy number of some typical cold response genes through duplication and/or lateral acquisition. At 77°C one third of the up-regulated genes are of hypothetical function, indicating that many features of high temperature growth are unknown.

scholarly journals Interactive Regulations of Dynamic Methylation and Transcriptional Responses to Recurring Environmental Stresses During Biological Invasions

2021 ◽  
Vol 8 ◽  
Author(s):  
Ruiying Fu ◽  
Xuena Huang ◽  
Yiyong Chen ◽  
Zaohuang Chen ◽  
Aibin Zhan
Keyword(s):  
Dna Methylation ◽  
Biological Invasions ◽  
Gene Transcription ◽  
Methylation Level ◽  
Environmental Stresses ◽  
Invasion Success ◽  
Transcriptional Level ◽  
Transcriptional Responses ◽  
Environmental Challenges ◽  
Stress Memory

Deoxyribonucleic acid methylation and gene transcription have been proved as two underlying mechanisms involved in rapid plastic response to environmental stresses. However, it remains elusive on how DNA methylation regulates gene transcription under acute and recurring environmental challenges to form the stress memory, further contributing to invasion success during range expansions. Using a model invasive species Ciona robusta, we investigated the regulatory roles of DNA methylation on gene transcription and their contribution to the formation of stress memory at 30 genes under acute and recurring osmotic challenges simulated during the invasion process. We found the bimodal distribution of methylation level for the 68 mCpGs identified across all the genes after challenges, but only five sites were significantly correlated with the expression of their corresponding genes. These genes participated in the biological processes of Ca2+ transport and metabolism of lipid and proline. At the DNA methylation level, we found two early-responding and four tardy-responding sites of stress memory and these sites were functionally related to genes involved in the biosynthesis of proline, metabolism of lipid, and transport of taurine and Ca2+. At the transcriptional level, three tardy-responding and five early-responding memory genes were involved in the transport of ions, regulation of water channels, biosynthesis of taurine, and metabolism of lipid. Altogether, the findings here suggest that DNA methylation and gene transcription should work in concert to facilitate the formation of stress memory, thus further improving the performance of invaders under recurring environmental challenges during biological invasions.

Age-related impairment of the transcriptional responses to oxidative stress in the mouse heart

2003 ◽  
Vol 13 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Michael G. Edwards ◽  
Deepayan Sarkar ◽  
Roger Klopp ◽  
Jason D. Morrow ◽  
Richard Weindruch ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Age Groups ◽  
Transcriptional Level ◽  
Mouse Heart ◽  
Mrna Levels ◽  
Middle Aged ◽  
Transcriptional Responses ◽  
Age Related ◽  
Young Mice

To investigate the transcriptional response to oxidative stress in the heart and how it changes with age, we examined the cardiac gene expression profiles of young (5-mo-old), middle-aged (15-mo-old), and old (25-mo-old) C57BL/6 mice treated with a single intraperitoneal injection of paraquat (50 mg/kg). Mice were killed at 0, 1, 3, 5, and 7 h after paraquat treatment, and the gene expression profile was obtained with high-density oligonucleotide microarrays. Of 9,977 genes represented on the microarray, 249 transcripts in the young mice, 298 transcripts in the middle-aged mice, and 256 transcripts in the old mice displayed a significant change in mRNA levels (ANOVA, P < 0.01). Among these, a total of 55 transcripts were determined to be paraquat responsive for all age groups. Genes commonly induced in all age groups include those associated with stress, inflammatory, immune, and growth factor responses. Interestingly, only young mice displayed a significant increase in expression of all three isoforms of GADD45, a DNA damage-responsive gene. Additionally, the number of immediate early response genes (IEGs) found to be induced by paraquat was considerably higher in the younger animals. These results demonstrate that, at the transcriptional level, there is an age-related impairment of specific inducible pathways in the response to oxidative stress in the mouse heart.

scholarly journals Adrenocorticotropic Hormone-Mediated Signaling Cascades Coordinate a Cyclic Pattern of Steroidogenic Factor 1-Dependent Transcriptional Activation

2006 ◽  
Vol 20 (1) ◽  
pp. 147-166 ◽  
Author(s):  
Jonathon N. Winnay ◽  
Gary D. Hammer
Keyword(s):  
Signaling Pathways ◽  
Transcriptional Activation ◽  
Hormone Receptors ◽  
Temporal Dynamics ◽  
Transcriptional Response ◽  
Endocrine Function ◽  
Signaling Cascades ◽  
Orphan Nuclear Receptor ◽  
Transcriptional Responses ◽  
Steroidogenic Factor 1

Abstract Steroidogenic factor 1 (SF-1) is an orphan nuclear receptor that has emerged as a critical mediator of endocrine function at multiple levels of the hypothalamic-pituitary-steroidogenic axis. Within the adrenal cortex, ACTH-dependent transcriptional responses, including transcriptional activation of several key steroidogenic enzymes within the steroid biosynthetic pathway, are largely dependent upon SF-1 action. The absence of a bona fide endogenous eukaryotic ligand for SF-1 suggests that signaling pathway activation downstream of the melanocortin 2 receptor (Mc2r) modulates this transcriptional response. We have used the chromatin immunoprecipitation assay to examine the temporal formation of ACTH-dependent transcription complexes on the Mc2r gene promoter. In parallel, ACTH-dependent signaling events were examined in an attempt to correlate transcriptional events with the upstream activation of signaling pathways. Our results demonstrate that ACTH-dependent signaling cascades modulate the temporal dynamics of SF-1-dependent complex assembly on the Mc2r promoter. Strikingly, the pattern of SF-1 recruitment and the subsequent attainment of active rounds of transcription support a kinetic model of SF-1 transcriptional activation, a model originally established in the context of ligand-dependent transcription by several classical nuclear hormone receptors. An assessment of the major ACTH-dependent signaling pathways highlights pivotal roles for the MAPK as well as the cAMP-dependent protein kinase A pathway in the entrainment of SF-1-mediated transcriptional events. In addition, the current study demonstrates that specific enzymatic activities are capable of regulating distinct facets of a highly ordered transcriptional response.

scholarly journals A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Bai ◽  
Emmanuel Caussinus ◽  
Stefano Leo ◽  
Fritz Bosshardt ◽  
Faina Myachina ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Low Temperature ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Transcriptional Level ◽  
Cool Temperature ◽  
Reporter Assay ◽  
Transcriptional Responses ◽  
General Response

Abstract Background Temperature change affects the myriad of concurrent cellular processes in a non-uniform, disruptive manner. While endothermic organisms minimize the challenge of ambient temperature variation by keeping the core body temperature constant, cells of many ectothermic species maintain homeostatic function within a considerable temperature range. The cellular mechanisms enabling temperature acclimation in ectotherms are still poorly understood. At the transcriptional level, the heat shock response has been analyzed extensively. The opposite, the response to sub-optimal temperature, has received lesser attention in particular in animal species. The tissue specificity of transcriptional responses to cool temperature has not been addressed and it is not clear whether a prominent general response occurs. Cis-regulatory elements (CREs), which mediate increased transcription at cool temperature, and responsible transcription factors are largely unknown. Results The ectotherm Drosophila melanogaster with a presumed temperature optimum around 25 °C was used for transcriptomic analyses of effects of temperatures at the lower end of the readily tolerated range (14–29 °C). Comparative analyses with adult flies and cell culture lines indicated a striking degree of cell-type specificity in the transcriptional response to cool. To identify potential cis-regulatory elements (CREs) for transcriptional upregulation at cool temperature, we analyzed temperature effects on DNA accessibility in chromatin of S2R+ cells. Candidate cis-regulatory elements (CREs) were evaluated with a novel reporter assay for accurate assessment of their temperature-dependency. Robust transcriptional upregulation at low temperature could be demonstrated for a fragment from the pastrel gene, which expresses more transcript and protein at reduced temperatures. This CRE is controlled by the JAK/STAT signaling pathway and antagonizing activities of the transcription factors Pointed and Ets97D. Conclusion Beyond a rich data resource for future analyses of transcriptional control within the readily tolerated range of an ectothermic animal, a novel reporter assay permitting quantitative characterization of CRE temperature dependence was developed. Our identification and functional dissection of the pst_E1 enhancer demonstrate the utility of resources and assay. The functional characterization of this CoolUp enhancer provides initial mechanistic insights into transcriptional upregulation induced by a shift to temperatures at the lower end of the readily tolerated range.

scholarly journals Transcriptional dynamics of bread wheat in response to nitrate and phosphate supply reveal functional divergence of genetic factors involved in nitrate and phosphate signaling

2019 ◽  
Author(s):  
Indeewari Dissanayake ◽  
Joel Rodriguez-Medina ◽  
Siobhan M. Brady ◽  
Miloš Tanurdžić
Keyword(s):  
Signaling Pathways ◽  
Functional Divergence ◽  
Nutrient Use Efficiency ◽  
Transcriptional Response ◽  
Transcriptional Responses ◽  
Wheat Roots ◽  
Wheat Varieties ◽  
Systemic Signaling ◽  
Nutrient Use ◽  
Gene Expression Dynamics

AbstractNitrate (N) and phosphate (P) levels are sensed by plant cells and signaled via local and systemic signaling pathways to modulate plant growth and development. Understanding the genetic basis of these signaling mechanisms is key to future improvement of nutrient use efficiency. While major progress has been made in understanding N and P signaling pathways and their interaction in the model plant Arabidopsis, understanding of transcriptional responses to N and P in a major monocot crop wheat is lacking. Therefore, we investigated gene expression dynamics of wheat roots in response to N and/or P provision using RNA-Seq. We found that nitrate presence is the major trigger for most of the transcriptional response to occur within 24 h, however, we also identified a large array of synergistic transcriptional responses to concomitant supply of N and P. Through gene co-expression analysis, we identified gene co-expression modules prominent in nitrate signaling and metabolism in wheat. Importantly, we identified likely instances of functional divergence in major N-responsive transcription factors families HRS1/HHO and TGA of wheat from their rice/Arabidopsis homologues. Our work broadens the understanding of wheat N and P transcriptional responses and aids in prioritizing gene candidates for production of wheat varieties that are efficient in nitrogen usage.

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